Contacts of the helix formed by residues 105 - 123 (chain B) in PDB entry 3CRL
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 ASP 105 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ASP* 3.6 22.1 - - + +
103B PRO 2.9 3.9 + - - +
104B GLU* 1.3 78.4 - - - +
106B HIS* 1.3 66.5 + - - +
107B ARG* 3.2 57.1 + - - +
108B THR* 3.2 26.2 + - - +
109B LEU* 3.2 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU* 4.4 17.7 + - - -
104B GLU 4.0 3.0 + - - -
105B ASP* 1.3 74.4 + - - +
107B ARG* 1.3 52.9 + - + +
109B LEU* 3.7 18.8 - - + +
110B SER* 2.7 43.4 + - - -
177B ASP* 5.1 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASP* 3.2 35.4 + - - +
106B HIS* 1.3 77.3 - - + +
108B THR* 1.3 61.5 + - - +
110B SER* 3.9 4.2 - - - -
111B GLN* 3.0 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 3.8 22.2 - - + -
98B PHE* 3.8 3.5 - - + -
101B LYS* 3.6 34.9 - - + +
102B ASP* 3.3 30.6 + - - +
103B PRO* 5.0 0.9 - - + -
105B ASP* 3.2 17.3 + - - +
107B ARG* 1.3 77.7 - - - +
109B LEU* 1.3 62.1 + - + +
111B GLN* 3.7 13.7 + - - +
112B PHE* 3.3 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU* 3.7 41.5 - - + +
47B LYS* 4.5 11.0 - - + +
50B PHE* 3.8 39.5 - - + -
103B PRO* 4.8 9.4 - - + -
104B GLU* 5.0 9.2 - - - +
105B ASP 3.2 16.2 + - - +
106B HIS* 3.8 22.2 - - + +
107B ARG 3.3 0.2 - - - -
108B THR* 1.3 76.1 - - - +
110B SER* 1.3 64.6 + - - +
112B PHE* 3.1 20.7 + - - +
113B THR* 3.3 13.5 + - - +
172B HIS* 5.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU* 5.2 1.6 - - - -
106B HIS* 2.7 27.8 + - - -
107B ARG* 3.9 4.9 - - - -
109B LEU* 1.3 73.0 - - - +
111B GLN* 1.3 60.9 - - - +
113B THR* 3.3 22.2 + - - -
114B ASP* 3.3 16.8 + - - +
177B ASP* 5.3 7.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
98B PHE* 3.5 23.5 - - + -
101B LYS* 5.1 9.0 - - - +
107B ARG* 3.0 33.2 + - - +
108B THR* 3.7 17.3 + - - +
110B SER* 1.3 74.3 - - - +
112B PHE* 1.3 61.8 + - - +
113B THR 3.4 0.2 - - - -
114B ASP* 3.6 14.7 - - + +
115B ALA* 3.1 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 3.4 41.7 - + + -
53B LEU* 3.8 23.8 - - + -
54B ARG* 4.1 15.3 - - + -
57B LEU* 4.9 0.4 - - + -
95B ILE* 4.7 10.8 - - + -
98B PHE* 3.5 26.0 - + + -
108B THR 3.3 16.1 + - - +
109B LEU 3.1 10.2 + - - +
111B GLN* 1.3 76.4 - - - +
113B THR* 1.3 57.8 + - - +
115B ALA* 3.2 5.1 + - + +
116B LEU* 3.0 55.5 + - + +
172B HIS* 3.6 34.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU* 3.9 12.1 - - - +
109B LEU 3.3 15.9 + - - +
110B SER* 3.3 10.5 + - - +
111B GLN 3.4 0.2 - - - -
112B PHE* 1.3 72.0 - - - +
114B ASP* 1.3 67.3 + - - +
116B LEU* 3.3 10.8 + - - +
117B VAL* 3.0 35.0 + - - +
172B HIS* 3.5 31.0 - - + +
173B THR* 4.2 9.3 - - - +
176B PHE* 4.7 10.3 - - + -
177B ASP* 5.0 6.8 + - - +
178B GLY* 5.0 9.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B SER* 3.3 20.0 + - - +
111B GLN* 3.6 16.3 - - - +
113B THR* 1.3 85.6 + - - +
115B ALA* 1.3 61.5 + - - +
117B VAL* 3.3 10.6 + - - +
118B THR* 3.1 25.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ASP* 5.0 12.0 - - + +
95B ILE* 6.0 1.3 - - + -
98B PHE* 3.8 23.3 - - + -
111B GLN 3.1 14.8 + - - +
112B PHE* 3.2 9.8 + - + +
114B ASP* 1.3 76.5 - - - +
116B LEU* 1.3 58.7 + - + +
118B THR* 3.3 7.9 + - - +
119B ILE* 2.9 36.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
53B LEU* 4.1 7.2 - - + -
57B LEU* 3.8 24.5 - - + -
95B ILE* 4.6 3.4 - - + -
112B PHE* 3.0 50.5 + - + +
113B THR* 3.7 6.5 - - - +
115B ALA* 1.3 73.8 - - + +
117B VAL* 1.3 61.6 + - - +
119B ILE* 3.3 17.0 + - + +
120B ARG* 2.9 30.5 + - - +
169B ILE* 3.8 30.4 - - + +
172B HIS* 3.9 30.3 - - + -
173B THR* 4.4 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B THR* 3.0 20.6 + - - +
114B ASP* 3.5 14.1 - - - +
116B LEU* 1.3 74.8 - - - +
118B THR* 1.3 59.8 + - - +
120B ARG* 3.3 30.6 + - - +
121B ASN* 3.0 44.2 + - - +
173B THR* 3.8 12.1 - - + -
178B GLY* 5.8 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ASP* 5.3 1.3 - - - +
114B ASP 3.1 14.3 + - - -
115B ALA* 3.6 10.8 - - - +
116B LEU 3.2 0.2 - - - -
117B VAL* 1.3 74.2 - - - +
119B ILE* 1.3 55.1 + - - +
121B ASN* 3.1 11.3 + - - +
122B ARG* 2.8 57.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 6.4 0.7 - - + -
91B SER* 3.4 33.2 - - - +
94B ASP* 4.5 7.9 - - + +
95B ILE* 3.6 37.5 - - + -
115B ALA* 2.9 22.7 + - + +
116B LEU* 3.5 13.5 - - + +
118B THR* 1.3 76.7 - - + +
120B ARG* 1.3 57.1 + - - +
122B ARG* 3.3 17.4 + - - +
123B HIS* 2.9 43.0 + - + +
165B ILE* 5.5 3.8 - - + -
169B ILE* 3.8 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU 2.9 16.1 + - - +
117B VAL* 3.6 32.5 + - - +
119B ILE* 1.3 77.6 - - - +
121B ASN* 1.3 67.4 + - - +
123B HIS* 3.5 3.8 + - - -
124B ASN* 3.3 25.9 + - - +
166B ARG* 3.2 42.1 + - + +
169B ILE* 4.1 15.5 - - + +
170B ASN* 2.8 22.8 + - - +
173B THR* 2.7 37.8 + - - +
174B LEU* 5.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B VAL* 3.0 35.1 + - - +
118B THR* 3.1 10.5 + - + +
120B ARG* 1.3 79.7 + - - +
122B ARG* 1.3 65.1 + - - +
124B ASN* 3.5 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TRP* 3.6 65.1 - - + +
90B GLN* 3.9 20.3 - - - +
91B SER* 3.2 24.9 + - - +
94B ASP* 2.6 32.1 + - - -
118B THR* 2.8 35.3 + - + +
119B ILE* 3.5 13.4 - - - +
121B ASN* 1.3 79.9 - - - +
123B HIS* 1.3 62.9 + - - +
124B ASN 3.2 3.7 + - - -
125B ASP 4.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 5.1 2.7 - - + +
87B TRP* 3.3 22.5 + - + -
88B TYR* 3.4 46.0 - + - -
91B SER* 2.6 32.6 + - - -
119B ILE* 2.9 33.2 + - + +
120B ARG* 3.5 6.0 + - - +
121B ASN 3.4 0.2 - - - -
122B ARG* 1.3 78.6 - - - +
124B ASN* 1.3 62.2 + - - +
125B ASP 3.3 2.9 - - - -
126B VAL* 3.2 29.5 + - + +
162B ARG* 3.3 19.6 + - + +
165B ILE* 6.4 2.2 - - + -
166B ARG* 5.0 2.7 - - + +
----------------------------------------------------------
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