Contacts of the helix formed by residues 118 - 133 (chain B) in PDB entry 1G8I
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 ARG 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B THR* 1.3 74.2 - - - +
119B ASN* 1.3 79.5 + - - +
121B MET* 3.2 3.5 + - - +
122B LEU* 2.8 43.2 + - - +
146B GLU* 4.0 28.7 - - - +
149B VAL* 3.6 18.0 - - + +
150B ASP* 3.3 27.2 + - - -
153B PHE* 3.6 22.6 - - + -
162B GLY* 3.3 16.9 + - - +
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Residues in contact with ASN 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B THR* 3.3 6.9 + - - +
118B ARG* 1.3 96.0 + - - +
120B GLU* 1.3 61.4 + - + +
122B LEU* 3.5 12.1 - - + +
123B ASP* 2.9 30.8 + - - +
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B TYR 3.5 14.0 - - - +
109B ASP* 4.0 0.2 - - - +
110B LEU* 3.7 24.0 - - + +
111B ASP* 2.9 29.0 + - - +
115B TYR 3.2 2.8 - - - +
116B ILE* 3.4 3.4 - - + -
117B THR* 2.9 36.9 + - - +
119B ASN* 1.3 75.6 - - - +
121B MET* 1.3 63.7 + - - +
123B ASP* 3.1 22.1 + - - +
124B ILE* 3.2 12.5 + - - +
1601B CA 2.4 30.9 - - - -
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Residues in contact with MET 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B TYR* 4.1 21.3 - - + -
116B ILE* 4.0 14.5 - - + +
117B THR 3.1 12.5 + - - +
118B ARG 3.7 7.0 - - - +
120B GLU* 1.3 76.3 - - - +
122B LEU* 1.3 58.4 + - - +
124B ILE* 3.2 2.1 + - - +
125B VAL* 2.9 41.8 + - + +
149B VAL* 4.0 13.2 - - + -
152B ILE* 3.7 31.9 - - + -
153B PHE* 3.7 14.8 - - + -
164B LEU* 4.1 19.3 - - + -
169B PHE* 4.5 7.6 - - + -
953B 1PE 3.8 28.5 - - - +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ARG* 2.8 39.3 + - - +
119B ASN* 3.5 13.9 - - - +
120B GLU 3.2 0.2 - - - -
121B MET* 1.3 75.9 - - - +
123B ASP* 1.3 56.9 + - - +
126B ASP* 2.9 35.7 + - + +
145B PRO* 3.8 13.7 - - + +
146B GLU* 3.8 52.3 - - + +
149B VAL* 3.6 11.2 - - + +
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Residues in contact with ASP 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LYS* 3.4 30.9 + - - +
67B PHE* 4.1 13.8 - - + -
110B LEU* 3.3 25.6 - - + +
119B ASN 2.9 14.1 + - - +
120B GLU* 3.2 11.0 - - - +
122B LEU* 1.3 77.0 - - - +
124B ILE* 1.3 59.0 + - - +
126B ASP* 3.6 0.4 + - - -
127B ALA* 3.0 23.9 + - - +
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B PHE* 4.0 19.3 - - + -
67B PHE* 3.5 37.9 - - + -
107B LEU* 3.8 17.9 - - + +
108B TYR* 3.1 50.7 - - + +
110B LEU* 3.8 18.2 - - + -
120B GLU 3.5 12.1 - - - +
121B MET 3.2 3.7 + - - +
123B ASP* 1.3 77.4 - - - +
125B VAL* 1.3 60.7 + - - +
127B ALA* 3.1 6.3 + - - +
128B ILE* 3.0 23.0 + - + +
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B TYR* 4.9 1.3 - - + +
121B MET* 2.9 25.7 + - + +
122B LEU 4.1 2.2 - - - +
124B ILE* 1.3 73.5 - - + +
126B ASP* 1.3 67.4 + - - +
128B ILE* 3.0 9.5 + - + +
129B TYR* 2.8 52.8 + - + -
145B PRO* 3.7 16.8 - - + +
148B ARG* 3.9 14.4 - - + -
149B VAL* 3.9 17.7 - - + -
953B 1PE 3.9 28.9 - - - +
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Residues in contact with ASP 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LYS* 2.6 27.6 + - - +
122B LEU* 2.9 21.2 + - + +
123B ASP* 3.8 3.4 - - - +
125B VAL* 1.3 77.1 - - - +
127B ALA* 1.3 56.3 + - - +
129B TYR* 3.1 3.1 + - - +
130B GLN* 2.8 52.8 + - - +
145B PRO* 3.8 25.7 - - + +
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Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ASP 4.7 1.0 - - - +
63B LYS* 3.7 22.6 - - + +
64B PHE* 3.6 35.6 + - + +
67B PHE* 3.9 6.3 - - + -
123B ASP 3.0 14.9 + - - +
124B ILE 3.1 9.2 + - - +
126B ASP* 1.3 76.1 + - - +
128B ILE* 1.3 57.8 + - - +
130B GLN* 3.4 4.8 + - - +
131B MET* 3.0 28.9 + - - +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B PHE* 3.9 31.9 - - + -
108B TYR* 4.3 9.9 - - - +
124B ILE* 3.0 21.0 + - + +
125B VAL* 3.0 10.5 + - + +
127B ALA* 1.3 74.9 - - - +
129B TYR* 1.3 74.6 + - + +
131B MET* 3.1 7.6 + - - +
132B VAL* 2.9 35.3 + - + +
953B 1PE 4.1 29.2 - - - -
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Residues in contact with TYR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B VAL* 2.8 35.5 + - + +
126B ASP* 3.7 7.2 - - - +
128B ILE* 1.3 83.8 - - + +
130B GLN* 1.3 59.8 + - + +
132B VAL* 3.2 6.9 + - - +
133B GLY* 2.8 30.8 + - - +
138B LEU* 3.7 22.7 - - + +
142B GLU* 2.7 32.8 + - - +
143B ASN 4.1 3.8 - - - -
144B THR* 3.7 26.5 + - - -
145B PRO* 3.9 19.1 - - + -
148B ARG* 3.8 14.8 - - + +
953B 1PE 6.1 0.9 - - - -
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Residues in contact with GLN 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLY* 3.5 2.4 - - - -
60B ASP* 3.0 42.2 + - + +
63B LYS* 4.0 17.5 + - + +
126B ASP* 2.8 48.1 + - - +
127B ALA* 3.7 5.8 - - - +
129B TYR* 1.3 73.1 - - + +
131B MET* 1.3 61.7 + - - +
133B GLY* 3.3 10.4 + - - +
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Residues in contact with MET 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B TYR* 3.6 16.4 - - + -
56B PHE* 3.6 49.3 - - + +
58B PHE 5.1 0.2 + - - -
59B GLY* 3.5 16.8 + - - -
60B ASP 3.7 8.9 + - - -
61B PRO* 3.2 41.3 - - + +
64B PHE* 3.1 44.4 - - + -
65B ALA 3.6 3.8 - - - +
127B ALA 3.0 16.3 + - - +
128B ILE* 3.1 6.3 + - - +
130B GLN* 1.3 77.9 - - - +
132B VAL* 1.3 62.7 + - + +
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B PHE* 4.7 22.0 - - + -
58B PHE* 4.2 17.5 - - - +
128B ILE* 2.9 32.5 + - + +
129B TYR* 3.7 5.4 - - - +
131B MET* 1.3 78.9 - - + +
133B GLY* 1.3 71.0 + - - +
135B THR* 4.6 4.0 + - - +
136B VAL* 6.0 6.7 - - + -
138B LEU* 5.8 7.4 - - + -
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Residues in contact with GLY 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B PHE 4.6 4.0 - - - -
59B GLY* 4.2 10.1 - - - -
129B TYR 2.8 16.0 + - - +
130B GLN* 3.8 9.6 - - - -
131B MET 3.3 2.0 - - - -
132B VAL* 1.3 94.2 - - - +
134B ASN* 1.3 62.2 + - - -
135B THR* 3.6 2.2 + - - -
136B VAL 5.1 0.3 + - - -
138B LEU* 5.5 4.0 - - - +
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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
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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) + - + + + + + -
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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