Contacts of the helix formed by residues 116 - 132 (chain B) in PDB entry 4GKH
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 SER 116 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B TYR* 2.8 34.2 + - - +
115B ASP* 1.3 79.8 - - - +
117B GLY* 1.3 62.9 + - - +
118B GLU 3.2 2.9 - - - -
119B ASN* 3.1 17.0 + - - +
120B ILE* 2.9 30.8 + - - +
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Residues in contact with GLY 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 3.6 24.0 - - - +
113B TYR 3.9 1.0 + - - -
114B PRO 3.3 13.0 + - - -
115B ASP 3.4 2.2 - - - -
116B SER* 1.3 75.9 - - - +
118B GLU* 1.3 57.1 + - - +
120B ILE* 3.3 1.9 + - - +
121B VAL* 2.9 33.8 + - - +
243B LEU* 3.8 16.2 - - - -
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Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ASP 5.2 0.8 + - - -
116B SER 3.2 0.8 - - - -
117B GLY* 1.3 75.8 - - - +
119B ASN* 1.3 58.1 + - - +
121B VAL* 3.4 1.6 + - - -
122B ASP* 3.0 33.6 + - - +
242B SER* 5.0 7.7 + - - +
243B LEU* 3.9 18.6 - - + -
246B ARG* 3.4 38.9 + - - +
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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
----------------------------------------------------------
116B SER* 3.1 19.4 + - - +
118B GLU* 1.3 75.7 - - - +
120B ILE* 1.3 66.4 + - + +
122B ASP* 3.3 15.1 + - - +
123B ALA* 3.1 21.8 + - - +
246B ARG* 5.5 0.7 + - - -
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Residues in contact with ILE 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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106B ALA* 5.0 3.1 - - + +
109B VAL* 3.6 31.9 - - + +
110B LEU* 3.7 42.8 - - + -
113B TYR* 4.1 8.7 - - + +
116B SER* 2.9 26.8 + - - +
117B GLY 3.6 4.3 - - - +
119B ASN* 1.3 75.4 - - + +
121B VAL* 1.3 63.4 + - + +
123B ALA* 3.2 8.4 + - - +
124B LEU* 3.0 33.8 + - + +
206B PHE* 3.9 26.0 - - + -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 5.6 1.1 - - + -
117B GLY 2.9 18.7 + - - +
118B GLU 3.8 3.8 - - - +
119B ASN 3.3 0.2 - - - -
120B ILE* 1.3 75.8 - - + +
122B ASP* 1.3 65.7 + - - +
124B LEU* 3.2 9.1 + - + +
125B ALA* 2.9 21.9 + - + +
236B LEU* 3.7 33.9 - - + -
243B LEU* 3.9 20.4 - - + +
246B ARG* 4.0 15.0 - - + +
247B LEU* 3.6 38.1 - - + +
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Residues in contact with ASP 122 (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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118B GLU 3.0 15.6 + - - +
119B ASN* 3.6 18.7 - - - +
120B ILE 3.3 0.4 - - - -
121B VAL* 1.3 74.3 - - - +
123B ALA* 1.3 58.0 + - - +
125B ALA* 3.4 3.0 + - - +
126B VAL* 3.0 34.4 + - + +
246B ARG* 2.8 41.1 + - - -
250B LYS* 3.1 31.4 + - + +
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Residues in contact with ALA 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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119B ASN 3.1 12.6 + - - +
120B ILE* 3.5 8.1 - - - +
121B VAL 3.2 0.2 - - - -
122B ASP* 1.3 75.2 - - - +
124B LEU* 1.3 64.3 + - - +
126B VAL* 3.3 7.7 + - - +
127B PHE* 3.0 24.8 + - - +
206B PHE* 4.3 21.5 - - + -
209B GLY 6.1 0.7 - - - +
211B LEU* 3.5 12.4 - - + +
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ALA* 4.2 9.2 - - + -
120B ILE* 3.0 31.2 + - + +
121B VAL* 3.6 19.1 - - + +
123B ALA* 1.3 75.2 - - - +
125B ALA* 1.3 57.9 + - - +
127B PHE* 3.3 2.6 + - - +
128B LEU* 2.9 30.0 + - - +
199B PHE* 4.4 3.7 - - + -
201B LEU* 3.7 24.7 - - + -
204B LEU* 3.5 36.3 - - + -
206B PHE* 4.4 1.8 - - + -
211B LEU* 3.8 18.4 - - + -
232B LEU* 4.1 22.0 - - + -
236B LEU* 4.7 3.1 - - + -
247B LEU* 5.0 3.1 - - + -
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Residues in contact with ALA 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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121B VAL 2.9 16.9 + - - +
122B ASP 3.7 4.5 - - - +
124B LEU* 1.3 78.1 - - - +
126B VAL* 1.3 62.3 + - + +
128B LEU* 3.4 4.4 + - - +
129B ARG* 3.0 28.9 + - - +
247B LEU* 4.0 19.8 - - + +
250B LYS* 3.7 27.6 - - + +
251B TYR* 3.8 15.8 - - - +
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ASP* 3.0 19.0 + - + +
123B ALA* 3.8 6.7 - - - +
124B LEU 3.3 0.2 - - - -
125B ALA* 1.3 76.3 - - + +
127B PHE* 1.3 64.3 + - - +
129B ARG* 3.2 14.3 + - + +
130B ARG* 3.1 25.6 + - + +
250B LYS* 6.1 1.1 - - + +
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Residues in contact with PHE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B MSE 3.5 23.3 - - + +
80B PRO* 3.8 24.9 - - + -
123B ALA 3.0 16.5 + - - +
124B LEU 3.6 3.1 - - - +
125B ALA 3.3 0.2 - - - -
126B VAL* 1.3 78.1 - - - +
128B LEU* 1.3 61.1 + - - +
130B ARG* 3.2 36.8 + - - +
131B LEU* 3.1 18.1 + - + +
199B PHE* 3.9 11.7 - + + -
204B LEU* 3.8 28.5 - - + -
211B LEU* 3.5 33.0 - - + -
213B GLY* 4.2 14.6 - - - -
214B CYS* 4.0 15.7 - - + -
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Residues in contact with LEU 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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124B LEU 2.9 17.1 + - - +
125B ALA* 3.9 5.4 - - - +
127B PHE* 1.3 77.8 - - - +
129B ARG* 1.3 61.7 + - - +
131B LEU* 3.4 4.6 + - + -
132B HIS* 3.0 53.5 + - + +
199B PHE* 3.8 34.5 - - + -
228B ASP* 3.7 26.5 - - + +
229B LEU* 3.7 34.3 - - + +
232B LEU* 5.0 0.9 - - + -
247B LEU* 5.0 7.9 - - + -
251B TYR* 3.9 9.0 - - + -
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Residues in contact with ARG 129 (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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125B ALA 3.0 23.0 + - - +
126B VAL* 3.2 12.5 + - + +
128B LEU* 1.3 76.7 - - - +
130B ARG* 1.3 57.7 + - - +
132B HIS* 3.5 3.8 + - - +
133B SER* 3.0 29.6 + - - -
250B LYS 3.8 14.5 + - - -
251B TYR* 2.8 55.9 + - + +
252B GLY* 4.4 5.5 - - - -
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Residues in contact with ARG 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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78B PHE 4.8 6.3 + - - +
79B MSE 3.5 17.7 - - - -
80B PRO* 4.0 22.2 - - - +
126B VAL* 3.1 16.1 + - + +
127B PHE* 3.5 42.8 - - - +
129B ARG* 1.3 75.3 - - - +
131B LEU* 1.3 65.2 + - - +
133B SER* 2.7 24.3 + - - +
134B ILE* 3.7 8.3 + - - +
211B LEU 4.9 4.8 + - - -
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Residues in contact with LEU 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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75B LEU* 4.0 22.9 - - + -
79B MSE 3.7 25.0 - - + +
127B PHE* 3.1 9.5 + - + +
128B LEU* 3.4 17.7 + - + +
130B ARG* 1.3 76.7 - - - +
132B HIS* 1.3 57.9 + - + +
133B SER 3.2 4.2 + - - -
134B ILE* 3.3 37.4 + - + +
194B VAL* 3.6 22.4 - - + +
195B THR 5.1 0.2 - - - -
196B HIS* 3.5 38.8 - - + +
199B PHE* 4.4 7.4 - - + -
228B ASP* 3.5 12.8 - - - +
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Residues in contact with HIS 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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128B LEU* 3.0 39.5 + - + +
129B ARG* 3.7 4.5 - - - +
130B ARG 3.3 0.2 - - - -
131B LEU* 1.3 76.9 - - + +
133B SER* 1.3 58.4 + - - +
134B ILE 3.4 4.6 + - - +
193B VAL* 3.6 29.5 - - + +
194B VAL 3.1 22.4 - - - -
195B THR* 4.2 0.8 - - - +
225B ARG* 3.5 38.6 + - + +
228B ASP* 2.9 26.3 + - + +
229B LEU* 4.9 0.4 - - + -
251B TYR* 2.6 33.4 + + + +
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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
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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