Contacts of the helix formed by residues 97 - 120 (chain B) in PDB entry 5CYP
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 97 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLY 5.6 0.8 + - - -
94A HIS 3.3 24.7 + - - -
95A ILE* 3.3 18.8 + - + +
97A ASN* 3.9 3.6 - - - +
91B PHE* 5.4 1.3 - - + +
92B GLY* 3.1 39.4 + - - +
93B ASP 3.6 2.6 + - - -
94B HIS* 3.6 21.1 + - - +
96B ASN* 1.3 74.4 - - - +
98B GLU* 1.3 65.1 + - - +
99B ASN 3.2 1.3 - - - -
100B CYS* 3.2 13.7 + - + +
101B TRP* 3.1 21.8 + - - +
150B LEU* 4.0 20.3 - - + +
154B PHE* 5.3 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 5.4 5.2 - - + +
96B ASN* 3.6 3.7 - - + -
97B ASN* 1.3 76.9 - - - +
99B ASN* 1.3 58.4 + - - +
100B CYS 3.0 5.4 + - - -
101B TRP* 3.3 7.4 + - - +
102B GLN* 3.2 23.9 + - - +
157B ARG* 5.0 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ASN* 4.5 11.3 + - + +
97B ASN 3.2 0.6 - - - -
98B GLU* 1.3 77.4 - - - +
100B CYS* 1.3 60.9 + - - +
102B GLN* 4.6 4.4 - - - +
103B PRO* 3.4 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PRO 5.8 0.3 - - - +
90B GLY 5.1 2.2 - - - +
91B PHE* 3.6 27.0 - - + +
93B ASP* 3.9 8.1 - - - -
94B HIS* 3.7 30.3 - - - -
96B ASN 4.6 2.5 - - - -
97B ASN* 3.2 22.8 + - - +
98B GLU 3.0 0.6 - - - -
99B ASN* 1.3 83.6 - - - +
101B TRP* 1.3 58.7 + - - +
102B GLN 3.2 4.9 - - - -
103B PRO* 3.4 13.0 - - - +
104B ILE* 4.2 15.9 - - - +
154B PHE* 4.5 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ASN 3.1 12.7 + - - +
98B GLU* 3.3 4.2 + - - +
100B CYS* 1.3 76.0 - - - +
102B GLN* 1.3 60.3 + - - +
104B ILE* 4.3 3.0 - - - +
105B MET* 3.1 30.0 + - + +
154B PHE* 3.5 35.8 - - + -
157B ARG* 3.2 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLU 3.2 15.4 + - - +
99B ASN* 4.6 4.9 - - - +
101B TRP* 1.3 76.0 - - - +
103B PRO* 1.4 73.8 - - + +
104B ILE 3.2 1.5 + - - -
105B MET* 3.3 5.1 + - - +
106B LYS* 3.0 24.5 + - - +
157B ARG* 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 3.6 23.1 - - + +
89B PRO* 5.9 5.8 - - + -
99B ASN 3.4 20.2 - - - +
100B CYS* 3.4 16.8 - - - +
102B GLN* 1.4 92.1 - - + +
104B ILE* 1.3 57.9 + - + +
106B LYS* 3.7 6.9 - - + +
107B PHE* 3.2 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B MET* 3.9 24.2 - - + -
29B VAL* 3.7 26.0 - - + -
67B ILE* 4.5 8.3 - - + -
88B THR* 4.0 21.8 - - + +
89B PRO* 4.7 7.9 - - + +
91B PHE* 4.4 11.2 - - + -
100B CYS 4.2 9.4 - - - +
101B TRP 4.3 6.3 - - - +
102B GLN 3.2 1.0 - - - -
103B PRO* 1.3 78.1 - - + +
105B MET* 1.3 64.7 + - - +
106B LYS 3.2 0.2 - - - -
107B PHE* 3.4 3.3 + - - +
108B ILE* 3.2 30.8 + - + +
154B PHE* 3.9 22.2 - - + -
158B LEU* 4.6 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TRP* 3.1 20.3 + - + +
102B GLN* 3.3 6.8 + - - +
104B ILE* 1.3 76.9 - - + +
106B LYS* 1.3 59.5 + - - +
108B ILE* 3.6 4.8 + - + +
109B ASN* 2.8 47.3 + - - +
154B PHE* 5.6 3.4 - - + -
157B ARG* 4.4 31.2 - - + +
158B LEU* 4.0 26.9 - - - -
161B VAL* 3.7 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLN 3.0 16.8 + - - +
103B PRO* 3.7 8.5 - - + +
104B ILE 3.2 0.2 - - - -
105B MET* 1.3 76.0 - - - +
107B PHE* 1.3 58.8 + - - +
109B ASN* 3.4 4.4 + - - +
110B ASP* 2.9 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B MET* 3.4 22.0 - - + -
67B ILE* 3.9 30.1 - - + -
69B SER* 3.8 23.1 - - - -
86B ILE* 3.7 28.7 - - + -
103B PRO 3.2 17.7 + - - +
104B ILE 3.4 4.9 + - - +
106B LYS* 1.3 77.8 - - - +
108B ILE* 1.3 62.8 + - - +
110B ASP* 3.3 7.0 + - + -
111B GLN* 3.1 62.2 + - + +
131B THR 5.3 0.9 - - - -
133B VAL* 4.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B MET* 4.2 17.0 - - + -
104B ILE* 3.2 18.6 + - + +
105B MET* 3.9 6.5 - - - +
107B PHE* 1.3 79.5 - - - +
109B ASN* 1.3 67.8 + - - +
111B GLN* 3.2 7.3 + - - +
112B TYR* 3.2 44.8 + - + +
133B VAL* 4.2 24.6 + - + -
136B CYS* 5.7 0.2 - - - -
158B LEU* 3.7 30.1 - - + -
161B VAL* 4.3 17.7 - - + +
162B VAL* 4.5 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B MET* 2.8 37.2 + - - +
106B LYS* 4.0 5.0 - - - +
108B ILE* 1.3 77.9 - - - +
110B ASP* 1.3 61.7 + - - +
112B TYR* 3.3 14.8 + - - +
113B GLU* 2.8 29.0 + - - +
161B VAL* 4.8 10.6 - - - +
285B TYR* 3.6 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LYS* 2.9 32.5 + - - +
107B PHE* 3.6 8.8 - - + +
108B ILE 3.2 0.2 - - - -
109B ASN* 1.3 77.9 - - - +
111B GLN* 1.3 62.7 + - - +
113B GLU* 3.2 9.2 + - - +
114B LYS* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PHE* 3.1 57.2 + - + +
108B ILE* 3.2 8.3 + - - +
110B ASP* 1.3 81.9 - - - +
112B TYR* 1.3 64.3 + - - +
113B GLU 3.1 0.4 - - - -
114B LYS* 3.4 6.0 + - - +
115B TYR* 3.1 25.6 + - - +
131B THR* 2.7 55.4 + - - +
132B ARG* 3.5 16.4 - - - +
133B VAL* 4.5 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ILE* 3.2 28.1 + - + -
109B ASN* 3.3 17.0 + - - +
111B GLN* 1.3 74.9 - - - +
113B GLU* 1.3 58.2 + - - +
116B LEU* 3.2 26.9 + - - +
132B ARG* 3.6 38.6 - - + -
133B VAL 3.8 15.7 + - - -
161B VAL* 2.9 33.0 + - + -
162B VAL* 4.3 2.3 - - - +
277B THR* 3.9 10.3 - - + +
281B HIS* 3.5 25.7 - - + +
282B PHE* 3.6 19.2 - + + -
285B TYR* 3.3 35.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASN 2.8 13.1 + - - +
110B ASP* 3.4 12.1 - - - +
111B GLN 3.1 0.2 - - - -
112B TYR* 1.3 74.5 - - - +
114B LYS* 1.3 59.6 + - - +
115B TYR 3.2 1.8 - - - -
116B LEU* 3.2 3.8 + - - +
117B GLN* 3.0 30.3 + - - +
285B TYR* 3.3 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASP 2.8 19.9 + - - +
111B GLN* 3.9 10.3 - - - +
113B GLU* 1.3 73.5 - - - +
115B TYR* 1.3 58.9 + - - +
117B GLN* 3.7 4.2 + - - -
118B GLU* 2.9 38.9 + - - +
128B ILE* 5.2 0.3 - - - +
131B THR* 4.5 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLN 3.1 17.5 + - - +
112B TYR 4.1 3.1 - - - +
114B LYS* 1.3 76.2 - - - +
116B LEU* 1.3 60.8 + - - +
117B GLN 3.3 0.2 - - - -
118B GLU* 3.4 2.6 + - - +
119B GLU* 3.1 48.0 + - + +
128B ILE* 3.8 37.1 + - + +
129B PRO 4.0 7.4 - - - -
130B ASP* 3.6 31.4 + - + +
131B THR* 4.7 1.8 + - - +
132B ARG* 3.6 47.5 + - + -
282B PHE* 3.9 10.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B TYR 3.2 18.9 + - - +
113B GLU* 3.2 5.8 + - - +
115B TYR* 1.3 77.8 - - - +
117B GLN* 1.3 59.8 + - - +
119B GLU* 3.9 8.2 - - + +
120B VAL* 3.0 28.3 + - + +
282B PHE* 3.9 21.5 - - + -
285B TYR* 3.8 22.2 - - + +
286B ARG* 4.5 18.8 - - + +
289B ARG* 4.2 18.6 - - + -
290B LEU* 6.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLU 3.0 16.7 + - - +
114B LYS* 4.1 3.4 - - - +
115B TYR 3.3 0.2 - - - -
116B LEU* 1.3 76.0 - - - +
118B GLU* 1.3 70.6 + - - +
120B VAL* 2.9 21.3 - - - +
121B ASN* 4.0 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LYS* 2.9 25.3 - - - +
115B TYR 3.4 2.1 + - - +
116B LEU 3.2 0.4 - - - -
117B GLN* 1.3 92.6 - - - +
119B GLU* 1.3 56.8 + - - +
120B VAL 2.9 13.4 - - - +
121B ASN* 3.6 10.9 - - - +
122B ILE* 5.3 0.3 - - - -
124B ARG* 5.7 2.1 - - - +
128B ILE* 3.3 44.9 - - + +
129B PRO* 5.1 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B TYR* 3.1 32.3 + - + +
116B LEU* 3.4 11.5 + - + +
118B GLU* 1.3 74.1 - - - +
120B VAL* 1.3 64.0 + - - +
121B ASN 4.0 0.2 + - - -
122B ILE* 4.3 12.3 + - - +
128B ILE* 3.8 15.3 - - + -
132B ARG* 5.3 0.2 + - - -
282B PHE* 3.2 32.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 3.0 19.5 + - + +
117B GLN* 2.9 10.5 - - - +
118B GLU 2.9 21.5 - - - +
119B GLU* 1.3 72.6 - - - +
121B ASN* 1.3 71.4 + - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il