Contacts of the helix formed by residues 104 - 120 (chain B) in PDB entry 2G3T
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 GLY 104 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 4.2 8.1 - - - -
103B PHE* 1.3 82.8 - - - +
105B ILE* 1.3 52.1 + - - +
106B GLY 3.3 2.9 - - - -
107B SER* 2.9 16.4 + - - -
108B GLU* 2.7 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 3.7 37.0 - - + -
6B ILE* 4.3 5.2 - - + -
57B ALA* 3.6 27.1 - - + -
59B VAL* 5.3 1.6 - - + -
72B VAL* 4.2 12.1 - - + -
73B GLY* 5.4 0.2 - - - -
96B VAL* 3.5 31.2 - - + -
100B TYR* 3.2 36.1 - - + +
101B ARG* 5.9 0.4 - - - -
103B PHE* 3.7 5.5 - - + -
104B GLY* 1.3 74.9 - - - +
106B GLY* 1.3 58.3 + - - +
108B GLU* 2.9 2.9 + - - +
109B ILE* 2.8 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B PHE* 3.9 26.0 - - - -
96B VAL* 3.9 7.8 - - - +
104B GLY 3.3 0.4 - - - -
105B ILE* 1.3 78.7 - - - +
107B SER* 1.3 61.2 + - - +
109B ILE* 3.2 11.8 + - - +
110B LEU* 3.1 26.7 + - - +
139B PHE* 5.1 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B GLY* 2.9 16.8 + - - -
106B GLY* 1.3 75.5 - - - +
108B GLU* 1.3 62.1 + - - +
110B LEU* 3.6 6.2 + - - +
111B LYS* 3.5 16.1 + - - +
139B PHE* 4.7 8.7 - - - -
143B ARG* 2.8 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 3.9 21.9 - - + -
6B ILE* 3.6 21.3 - - + -
104B GLY 2.7 16.5 + - - +
105B ILE 3.4 7.2 - - - +
107B SER* 1.3 73.2 + - - +
109B ILE* 1.3 66.1 + - - +
111B LYS* 3.3 24.9 + - - +
112B ASN* 3.0 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 3.3 37.0 - - + -
55B LEU* 4.6 5.8 - - + -
56B VAL 5.3 0.4 - - - -
57B ALA* 4.6 7.9 - - + +
73B GLY 5.8 0.2 - - - -
74B PHE 5.3 7.6 - - - +
75B ALA* 3.4 34.1 - - + -
94B PHE* 4.4 14.4 - - + -
96B VAL* 5.1 2.5 - - + -
105B ILE* 2.8 28.7 + - + +
106B GLY* 3.4 12.1 - - - +
108B GLU* 1.3 77.6 - - - +
110B LEU* 1.3 64.6 + - + +
112B ASN* 3.1 8.1 + - - +
113B LEU* 2.9 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 4.5 2.2 - - + -
94B PHE* 3.8 29.4 - - + -
106B GLY 3.1 17.2 + - - +
107B SER* 3.7 10.1 - - - +
108B GLU 3.3 0.2 - - - -
109B ILE* 1.3 83.7 - - + +
111B LYS* 1.3 56.1 + - - +
113B LEU* 3.7 11.8 - - + +
114B SER* 2.9 35.7 + - - +
125B MET* 4.0 27.6 - - + -
139B PHE* 4.4 17.5 - - + -
140B TYR* 4.0 19.1 - - + +
143B ARG* 4.9 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B SER 3.5 9.3 + - - +
108B GLU* 3.3 31.5 + - - +
109B ILE 3.2 0.6 - - - -
110B LEU* 1.3 78.4 - - - +
112B ASN* 1.3 59.9 + - - +
114B SER* 3.2 8.0 + - - -
115B GLN* 3.0 55.8 + - + +
143B ARG* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 3.3 37.4 - - + +
55B LEU* 3.7 20.6 - - + +
108B GLU* 3.0 29.5 + - - +
109B ILE 3.1 8.3 + - - +
111B LYS* 1.3 77.4 - - - +
113B LEU* 1.3 66.0 + - - +
115B GLN* 3.2 21.3 + - - +
116B VAL* 3.0 24.9 + - - +
119B ARG* 5.1 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 3.8 15.9 - - + -
75B ALA* 4.4 5.2 - - + -
77B TYR* 3.6 39.7 - - + -
89B LEU* 3.4 13.9 - - + +
91B LEU* 3.7 35.9 - - + -
109B ILE* 2.9 34.7 + - + +
110B LEU* 3.7 14.4 - - + +
112B ASN* 1.3 75.6 - - - +
114B SER* 1.3 63.3 + - - +
116B VAL* 3.0 9.2 + - + +
117B ALA 3.0 18.5 + - - -
125B MET* 4.3 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 2.9 24.4 + - - +
111B LYS* 3.4 8.0 - - - -
113B LEU* 1.3 78.3 - - - +
115B GLN* 1.3 62.2 + - - +
117B ALA* 3.3 9.2 + - - +
118B MET* 3.0 29.4 + - - +
125B MET* 5.3 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LYS* 3.0 42.8 + - + +
112B ASN* 3.4 32.7 + - - +
113B LEU 3.1 0.4 - - - -
114B SER* 1.3 73.5 - - - +
116B VAL* 1.3 66.4 + - - +
118B MET* 3.3 8.8 + - - +
119B ARG* 3.0 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 5.1 8.3 - - + -
77B TYR* 3.8 44.0 - - + +
79B PHE* 4.1 9.4 - - + -
89B LEU* 4.4 6.7 - - + -
112B ASN 3.0 18.4 + - - +
113B LEU* 3.0 14.0 + - + +
115B GLN* 1.3 77.5 - - - +
117B ALA* 1.3 57.3 + - - +
119B ARG* 3.3 21.9 + - - +
120B CYS* 2.9 51.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU* 3.7 23.5 - - + +
113B LEU 3.0 6.7 + - - +
114B SER* 3.4 12.8 - - - +
116B VAL* 1.3 79.6 - - - +
118B MET* 1.3 64.5 + - + +
120B CYS 3.9 0.2 - - - -
121B ARG* 3.4 2.6 + - - -
122B CYS* 3.1 49.1 + - + +
124B SER* 5.4 4.3 - - - +
125B MET* 5.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 5.7 3.4 - - - +
115A GLN* 4.0 23.3 - - - +
114B SER* 3.0 18.4 + - - +
115B GLN* 3.7 9.2 - - - +
116B VAL 3.3 0.2 - - - -
117B ALA* 1.3 81.5 - - - +
119B ARG* 1.3 58.8 + - + +
120B CYS 3.7 0.2 + - - -
121B ARG* 3.9 6.9 + - - -
122B CYS 5.5 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASN 5.3 0.4 + - - -
115B GLN* 3.0 38.7 + - - +
116B VAL* 3.6 32.3 - - - +
118B MET* 1.3 76.7 - - - +
120B CYS* 1.3 71.5 + - - +
121B ARG* 3.3 2.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 3.8 28.7 - - + -
87B LYS* 2.9 33.9 + - - +
116B VAL* 2.9 35.4 + - - +
117B ALA 3.5 0.2 + - - -
119B ARG* 1.3 92.1 - - - +
121B ARG* 1.3 66.7 + - - +
122B CYS* 3.4 4.0 - - - -
----------------------------------------------------------
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