Contacts of the helix formed by residues 102 - 117 (chain B) in PDB entry 2GOJ
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 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B ILE* 3.9 7.7 - - - +
97B GLN* 4.3 9.6 - - - +
100B PHE* 3.1 5.7 + - - +
101B GLY* 1.3 77.6 - - - +
103B PHE* 1.3 64.1 + - - +
104B ASN* 3.6 7.7 + - - +
105B ASN* 3.1 31.3 + - - +
106B PHE* 3.1 21.3 + - - +
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Residues in contact with PHE 103 (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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86B GLY 3.8 20.6 - - - -
87B GLU* 3.6 34.3 - - - +
88B PRO* 3.5 28.0 - - + -
93B LYS* 6.4 0.4 - - + -
96B ILE* 3.8 11.9 - - + +
97B GLN* 4.8 6.1 - - + +
102B SER* 1.3 73.9 - - - +
104B ASN* 1.3 66.4 + - - +
106B PHE* 3.1 13.2 + + - +
107B LYS* 2.8 57.6 + - + +
179B TRP* 4.0 17.9 - + + -
184B TRP* 3.5 28.0 - + - -
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Residues in contact with ASN 104 (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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87B GLU* 4.5 5.7 - - - +
102B SER* 3.3 6.9 + - - +
103B PHE* 1.3 92.3 - - - +
105B ASN* 1.3 63.1 + - - +
107B LYS* 3.6 11.6 + - - +
108B GLU* 3.0 38.1 + - - +
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Residues in contact with ASN 105 (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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100B PHE* 3.1 27.9 + - + +
101B GLY* 4.3 4.0 - - - -
102B SER* 3.1 24.3 + - - +
104B ASN* 1.3 76.9 - - - +
106B PHE* 1.3 64.1 + - - +
108B GLU* 4.0 3.1 - - - +
109B GLN* 3.1 27.3 + - - +
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Residues in contact with PHE 106 (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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96B ILE* 3.7 40.4 - - + -
100B PHE* 3.7 33.8 - + + +
102B SER 3.1 2.9 + - - +
103B PHE* 3.1 18.8 + + - +
105B ASN* 1.3 77.1 - - - +
107B LYS* 1.3 62.7 + - - +
109B GLN* 3.3 2.6 + - - +
110B PHE* 2.9 50.1 + + + +
125B LEU* 3.7 39.7 - - + -
135B ILE* 3.9 20.0 - - + -
154B LEU* 5.7 2.9 - - + -
179B TRP* 3.7 22.4 - + - -
184B TRP* 4.3 6.5 - + - -
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Residues in contact with LYS 107 (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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103B PHE* 2.8 49.1 + - + +
104B ASN* 3.6 13.6 + - - +
106B PHE* 1.3 74.9 - - - +
108B GLU* 1.3 58.2 + - + +
111B SER* 2.6 39.2 + - - +
176B LYS* 6.3 2.6 - - - +
179B TRP* 3.5 55.7 - - + +
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Residues in contact with GLU 108 (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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104B ASN* 3.0 26.4 + - - +
105B ASN* 4.1 3.6 - - - +
107B LYS* 1.3 79.4 - - + +
109B GLN* 1.3 66.2 + - - +
111B SER* 3.4 5.9 + - - -
112B ASN* 3.0 33.6 + - - +
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Residues in contact with GLN 109 (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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100B PHE* 3.6 25.2 - - - -
105B ASN 3.1 18.0 + - - +
106B PHE 3.7 2.9 - - - +
108B GLU* 1.3 76.8 - - - +
110B PHE* 1.3 61.9 + - - +
112B ASN* 3.3 10.0 + - - +
113B ILE* 3.2 35.9 + - + +
135B ILE* 3.7 19.8 - - + +
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Residues in contact with PHE 110 (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 PHE* 2.9 31.9 + + + +
107B LYS 4.0 2.7 - - - +
109B GLN* 1.3 73.0 - - - +
111B SER* 1.3 57.8 + - - +
113B ILE* 3.2 5.4 + - + +
114B LEU* 2.9 56.5 + - + +
123B GLY* 3.8 26.5 - - - -
124B TRP 3.4 33.2 - - - -
125B LEU* 4.2 5.2 - - + -
135B ILE* 3.6 32.3 - - + +
154B LEU* 5.3 2.9 - - + -
155B THR 5.4 0.4 - - - -
156B CYS* 4.6 2.7 - - + -
178B TRP* 3.8 22.9 - + - -
179B TRP* 3.6 26.0 - + + -
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Residues in contact with SER 111 (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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107B LYS* 2.6 26.2 + - - +
108B GLU* 3.7 6.7 - - - -
109B GLN 3.3 0.2 - - - -
110B PHE* 1.3 75.5 - - - +
112B ASN* 1.3 59.3 + - - +
114B LEU* 3.5 1.8 + - - +
115B CYS* 2.9 38.5 + - - +
175B VAL* 3.8 18.9 - - - +
179B TRP* 3.0 23.1 + - - -
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Residues in contact with ASN 112 (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 GLU* 3.0 22.7 + - - +
109B GLN* 3.5 11.7 - - + +
110B PHE 3.2 0.2 - - - -
111B SER* 1.3 77.7 - - - +
113B ILE* 1.3 60.4 + - + +
115B CYS* 3.8 4.1 - - - +
116B GLY* 2.8 26.9 + - - -
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Residues in contact with ILE 113 (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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109B GLN* 3.2 35.1 + - + +
110B PHE* 3.2 8.8 + - + +
112B ASN* 1.3 78.2 - - + +
114B LEU* 1.3 66.6 + - + +
116B GLY* 3.9 1.5 - - - -
117B HIS* 3.2 24.4 + - - +
123B GLY* 5.6 3.1 - - - -
135B ILE* 3.5 33.4 - - + +
136B LEU 4.9 1.8 - - - +
137B GLN* 4.0 40.9 - - + +
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Residues in contact with LEU 114 (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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110B PHE* 2.9 48.0 + - + +
111B SER* 3.8 3.6 - - - +
113B ILE* 1.3 75.4 - - + +
115B CYS* 1.3 58.8 + - - +
117B HIS* 3.7 5.3 + - - +
123B GLY* 3.6 35.7 - - - +
156B CYS* 3.9 26.7 - - + -
158B ILE* 3.9 16.8 - - + +
171B ARG* 2.8 29.7 + - - -
175B VAL* 3.8 31.0 - - + -
178B TRP* 4.8 4.7 - - + -
179B TRP* 5.3 0.2 - - + -
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Residues in contact with CYS 115 (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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111B SER* 2.9 26.0 + - - +
112B ASN* 4.0 4.3 - - - +
114B LEU* 1.3 76.5 - - - +
116B GLY* 1.3 60.9 + - - +
117B HIS 4.5 0.2 - - - +
171B ARG* 3.4 18.2 + - + +
172B ALA* 3.6 38.6 - - - -
175B VAL* 4.0 16.6 - - - -
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Residues in contact with GLY 116 (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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112B ASN 2.8 18.0 + - - -
113B ILE* 3.3 3.7 + - - -
115B CYS* 1.3 75.4 - - - +
117B HIS* 1.3 63.9 + - - +
118B PHE* 3.3 5.7 + - - +
137B GLN* 5.1 1.6 - - - -
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Residues in contact with HIS 117 (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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113B ILE 3.2 15.9 + - - +
114B LEU* 4.0 2.0 - - - +
115B CYS 3.3 2.4 - - - +
116B GLY* 1.3 76.7 - - - +
118B PHE* 1.3 64.5 + - - +
119B GLY 3.4 10.1 - - - -
120B SER 3.2 7.6 + - - -
121B GLY* 4.0 1.3 - - - -
122B TRP 5.4 1.3 - - - -
137B GLN* 3.2 32.5 + - + +
138B THR 3.6 21.6 + - - -
139B HIS* 3.0 32.8 + + + -
158B ILE* 3.2 31.2 - - + -
171B ARG* 2.8 36.5 + - - +
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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