Contacts of the helix formed by residues 94 - 110 (chain B) in PDB entry 6D6Q
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 LYS 94 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ARG* 3.7 34.1 - - - +
75B TYR* 5.5 9.9 - - - -
77B SER* 5.9 5.3 + - - -
86B LYS* 5.4 6.9 - - - +
92B ASP* 3.2 15.7 + - - +
93B ARG* 1.3 78.5 - - - +
95B SER* 1.3 68.2 + - - +
96B CYS 3.1 1.1 - - - -
97B GLU* 3.1 5.9 + - - +
98B MET* 3.0 41.2 + - + +
42O C 4.4 2.9 + - - +
43O A 4.9 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TYR* 3.5 45.2 + - - +
89B PRO 3.5 25.1 + - - -
90B HIS* 4.0 0.7 - - - -
91B GLY 3.8 7.6 + - - -
92B ASP* 3.6 18.7 + - - +
94B LYS* 1.3 80.2 - - - +
96B CYS* 1.3 61.6 + - - +
98B MET* 3.3 3.3 + - - +
99B GLY* 2.9 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP* 5.7 3.5 - - - +
100A VAL* 4.3 22.0 - - + -
91B GLY* 4.5 14.1 - - - -
92B ASP 3.4 20.1 + - - +
94B LYS 3.1 1.0 - - - -
95B SER* 1.3 82.7 + - - +
97B GLU* 1.3 61.1 + - - +
99B GLY* 3.2 2.5 + - - +
100B LEU* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A VAL* 3.9 13.0 - - + +
101A LYS* 5.1 9.2 - - + +
104A ARG* 2.9 48.1 + - + +
105A LEU 5.0 1.7 + - - -
108A ARG* 4.1 13.0 + - - -
235A GLN* 4.1 15.4 + - - +
93B ARG 4.0 7.9 - - - +
94B LYS* 3.1 11.4 + - + +
96B CYS* 1.3 76.1 - - - +
98B MET* 1.3 68.8 + - + +
100B LEU* 3.2 10.9 + - + +
101B GLN* 2.9 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TYR* 3.6 40.8 - - + +
94B LYS* 3.0 36.0 + - + +
95B SER 3.5 7.9 - - - +
97B GLU* 1.3 79.0 - - - +
99B GLY* 1.3 58.1 + - - +
101B GLN* 3.3 17.8 + - - +
102B LEU* 2.9 35.2 + - + +
134B TYR* 3.4 38.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B CYS* 2.9 30.4 - - - -
75B TYR* 4.3 7.5 - - - +
95B SER 2.9 15.2 + - - -
96B CYS* 3.2 4.9 + - - -
97B GLU 3.2 0.2 - - - -
98B MET* 1.3 75.4 - - - +
100B LEU* 1.3 61.4 + - - +
102B LEU* 4.8 1.3 - - - -
103B ARG* 2.9 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP* 3.7 49.6 - - + +
100A VAL* 5.0 2.0 - - + -
101A LYS* 4.1 23.1 - - + +
96B CYS 2.9 18.6 + - - +
97B GLU* 3.2 14.3 + - + +
99B GLY* 1.3 74.7 - - - +
101B GLN* 1.3 65.2 + - + +
103B ARG* 3.2 38.3 + - - +
104B GLN* 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 5.1 0.4 - - - +
235A GLN* 4.5 3.5 - - - +
97B GLU* 2.9 39.8 + - + +
98B MET* 3.4 23.3 - - - +
99B GLY 3.2 0.2 - - - -
100B LEU* 1.3 77.5 - - + +
102B LEU* 1.3 64.6 + - - +
103B ARG 3.1 0.2 + - - -
104B GLN* 3.2 10.2 + - - +
105B THR* 3.0 26.5 + - - +
134B TYR* 3.4 32.8 - - + +
197B LEU* 4.2 6.7 - - + -
199B GLU* 3.0 46.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B CYS* 3.6 21.3 - - + -
74B GLN 4.9 4.0 - - - +
75B TYR* 4.7 14.8 - - + -
98B MET* 2.9 24.6 + - + +
99B GLY* 5.0 0.9 - - - -
101B GLN* 1.3 73.1 - - - +
103B ARG* 1.3 57.4 + - - +
105B THR* 2.4 21.3 + - - -
106B PHE* 3.0 38.1 + - + -
122B ILE* 5.4 0.9 - - + -
124B VAL* 4.0 29.8 - - + -
134B TYR* 3.5 29.6 + - + +
137B CYS* 4.9 2.9 - - + -
138B VAL* 3.8 22.0 - - + +
141B ALA* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP* 4.0 18.2 + - - +
71B VAL* 3.6 30.0 - - + +
72B ASN* 5.1 0.9 - - - +
73B CYS* 3.2 17.2 - - - +
99B GLY 2.9 19.0 + - - +
100B LEU* 3.2 34.2 + - - +
102B LEU* 1.3 76.8 - - - +
104B GLN* 1.3 57.0 + - - +
106B PHE* 4.4 0.2 - - - +
107B GLU* 2.9 57.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A SER* 3.9 8.0 + - - +
237A SER* 3.9 5.7 - - - -
238A GLY* 3.5 14.5 + - - +
239A GLY* 2.4 66.4 + - - +
240A ILE* 4.1 0.9 + - - +
100B LEU 2.9 15.7 + - - +
101B GLN* 3.3 11.5 + - - +
103B ARG* 1.3 75.9 - - - +
105B THR* 1.3 75.4 + - - +
107B GLU* 4.2 9.1 - - - +
108B ALA* 3.6 6.9 + - - +
196B ALA 3.5 17.2 + - - +
197B LEU* 3.3 31.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLN 3.0 16.4 + - - +
102B LEU* 2.4 28.4 + - - +
104B GLN* 1.3 91.6 - - - +
106B PHE* 1.3 69.6 + - - -
108B ALA* 2.9 23.0 + - - +
109B ALA* 3.0 13.4 + - - +
134B TYR* 3.9 4.2 + - - +
138B VAL* 5.6 3.6 - - + +
156B VAL* 5.1 9.4 - - - +
187B ALA* 5.1 4.9 - - + -
196B ALA* 4.0 16.9 - - + +
197B LEU* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 4.8 5.2 - - + -
102B LEU* 3.0 44.6 + - + +
103B ARG 4.4 0.9 - - - +
105B THR* 1.3 86.7 + - - +
107B GLU* 1.3 59.8 + - - +
109B ALA* 4.1 7.0 - - + +
110B ILE* 2.5 46.9 + - + +
122B ILE* 4.1 25.6 - - + -
138B VAL* 3.6 16.6 - - + -
141B ALA* 3.5 32.8 - - + -
142B THR* 3.7 13.5 - - - -
145B VAL* 4.7 12.1 - - + -
152B MET* 5.1 5.2 - - + -
156B VAL* 3.7 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLY* 6.1 0.9 - - - -
68B ARG* 5.7 5.2 + - - +
69B ALA 5.5 2.0 - - - +
70B LEU* 5.7 2.3 - - - +
71B VAL* 3.4 33.9 + - + +
103B ARG* 2.9 51.6 + - - +
104B GLN* 4.5 7.0 - - - +
106B PHE* 1.3 76.6 - - - +
108B ALA* 1.3 60.7 + - - +
110B ILE* 4.2 10.1 + - - +
111B LEU* 4.7 1.6 + - - -
112B THR* 4.6 11.2 + - + +
153B ARG* 4.7 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLY* 3.9 16.1 - - - +
240A ILE 4.6 0.2 - - - +
241A MET* 3.2 35.5 - - + +
104B GLN 3.6 12.7 + - - +
105B THR* 2.9 15.3 + - - +
107B GLU* 1.3 79.0 - - - +
109B ALA* 1.3 50.6 - - + +
153B ARG* 2.1 35.0 + - - -
196B ALA* 5.1 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A MET* 4.8 2.5 - - - -
105B THR 3.0 13.0 + - - +
106B PHE* 4.2 6.7 - - + +
108B ALA* 1.3 76.0 - - + +
110B ILE* 1.3 58.4 + - - +
111B LEU 2.8 12.6 + - - -
152B MET* 4.4 7.6 - - + -
153B ARG* 3.1 33.8 + - + +
154B ASP 4.7 6.5 - - - +
156B VAL* 4.5 15.5 - - + -
189B LEU* 4.4 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 4.3 8.3 - - + -
106B PHE* 2.5 40.2 + - + +
107B GLU* 4.2 1.8 - - - -
108B ALA 3.7 0.2 - - - -
109B ALA* 1.3 71.3 - - - +
111B LEU* 1.3 63.5 + - - +
112B THR* 3.1 32.2 - - + -
115B HIS* 5.6 0.3 - - - -
120B ILE* 4.2 17.2 - - + +
122B ILE* 5.9 1.1 - - + -
145B VAL* 3.2 43.3 - - + -
150B ILE* 3.3 23.8 - - + +
151B PRO* 2.5 24.8 - - - +
152B MET* 4.1 6.5 - - + -
----------------------------------------------------------
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