Contacts of the helix formed by residues 107 - 122 (chain B) in PDB entry 6GYS
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 GLN 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B ASN 4.6 9.8 + - - +
105B TYR 4.7 0.9 + - - +
106B LEU* 1.3 79.6 - - - +
108B LYS* 1.3 58.1 + - - +
109B ASP* 3.6 13.5 - - - +
110B GLN* 2.4 41.3 + - - +
111B SER* 2.7 34.1 + - - -
144B TRP* 3.4 10.8 - - + -
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Residues in contact with LYS 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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107B GLN* 1.3 75.0 - - - +
109B ASP* 1.3 61.5 + - - +
111B SER* 2.3 25.6 + - - -
112B PHE* 2.9 27.2 + - + -
141B GLU* 2.8 41.6 + - - +
144B TRP* 3.5 54.5 + - + +
145B ASP* 4.4 10.3 + - - -
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Residues in contact with ASP 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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107B GLN* 3.7 15.7 - - - +
108B LYS* 1.3 72.1 - - - +
110B GLN* 1.3 83.8 + - - +
112B PHE* 3.3 7.0 + - - +
113B GLN* 2.9 45.6 + - - +
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Residues in contact with GLN 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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105B TYR 3.0 17.1 + - - +
106B LEU* 3.6 4.0 - - + -
107B GLN* 2.4 55.4 + - - +
109B ASP* 1.3 91.5 + - - +
111B SER* 1.3 60.8 + - - +
113B GLN* 3.6 1.3 + - - +
114B LEU* 3.4 25.8 + - - +
182B ILE* 3.7 31.1 + - + +
183B PHE* 3.2 27.8 - - + +
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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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106B LEU* 3.6 14.6 - - - +
107B GLN 2.7 17.1 + - - -
108B LYS 2.3 26.5 + - - -
110B GLN* 1.3 74.9 - - - +
112B PHE* 1.3 63.7 + - - +
114B LEU* 3.1 8.2 + - - +
115B MET* 2.9 29.9 + - - +
140B VAL* 4.0 2.8 - - - +
144B TRP* 3.3 17.1 + - - -
167B PHE* 3.6 27.3 - - - -
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Residues in contact with PHE 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 LYS* 2.9 40.1 + - + +
109B ASP* 4.1 6.1 - - - +
111B SER* 1.3 78.6 + - - +
113B GLN* 1.3 60.9 + - + +
115B MET* 3.5 8.3 - - + +
116B ASN* 2.8 40.2 + - - +
137B TYR* 4.1 37.7 - + + -
140B VAL* 3.6 26.2 - - + -
141B GLU* 2.9 36.8 - - + -
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Residues in contact with GLN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASP* 2.9 29.5 + - - +
110B GLN* 4.0 4.1 - - - +
111B SER 3.3 0.2 - - - -
112B PHE* 1.3 77.6 - - + +
114B LEU* 1.3 61.1 + - - +
116B ASN* 3.6 14.1 + - - +
117B PHE* 3.5 17.7 + - - +
174B MET* 4.5 0.5 - - - +
181B GLU 4.3 3.2 + - - +
182B ILE* 3.3 46.8 - - + +
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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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106B LEU* 4.3 16.8 - - + -
110B GLN 3.4 15.7 + - - +
111B SER 3.1 7.0 + - - +
113B GLN* 1.3 77.2 - - - +
115B MET* 1.3 58.9 + - - +
117B PHE* 3.1 6.4 + - - +
118B ALA 2.9 23.2 + - - -
167B PHE* 4.0 31.0 - - + +
170B CYS* 3.6 29.6 - - + -
171B ILE* 4.4 9.4 - - + -
174B MET* 3.7 24.9 - - + -
179B LEU* 4.4 9.9 - - + -
182B ILE* 4.4 2.0 - - + -
183B PHE* 4.3 20.0 - - + -
212B PHE* 6.0 2.2 - - + -
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Residues in contact with MET 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 20.9 + - - +
112B PHE* 3.2 14.8 + - + +
114B LEU* 1.3 76.8 - - - +
116B ASN* 1.3 57.6 + - - +
118B ALA* 3.3 7.5 + - - +
119B MET* 2.9 23.7 + - - +
133B ILE* 3.4 27.8 - - + +
136B LEU* 3.7 24.7 - - + -
137B TYR* 3.5 37.5 - - + -
140B VAL* 4.6 9.2 - - + -
163B ILE* 6.4 0.7 - - - -
166B VAL* 3.9 17.7 - - + -
167B PHE* 3.5 26.7 - - + -
170B CYS* 4.9 0.7 - - - -
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Residues in contact with ASN 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 PHE* 2.8 32.2 + - - +
113B GLN* 3.6 15.5 - - - +
115B MET* 1.3 75.2 - - - +
117B PHE* 1.3 56.6 + - - +
119B MET* 3.1 22.1 + - + +
120B GLU* 2.8 36.0 + - - +
137B TYR* 4.0 12.2 + - - -
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Residues in contact with PHE 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 GLN 3.5 5.6 + - - +
114B LEU 3.1 10.2 + - - +
116B ASN* 1.3 75.1 - - - +
118B ALA* 1.3 66.7 + - - +
120B GLU* 3.2 29.3 + - - +
121B ASN* 3.0 43.2 + - - +
122B LEU* 4.2 12.1 + - + -
170B CYS* 4.3 7.9 - - - -
173B TYR* 3.2 37.7 - - + -
174B MET* 3.6 37.2 - - + -
175B PRO* 3.6 20.9 - - + -
178B LYS* 4.9 14.8 - - + -
452B PHE* 4.1 9.2 - + - -
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Residues in contact with ALA 118 (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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114B LEU 2.9 6.2 + - - +
115B MET* 3.3 15.3 - - - +
116B ASN 3.2 0.2 - - - -
117B PHE* 1.3 77.1 - - - +
119B MET* 1.3 59.5 + - - +
122B LEU* 2.9 41.3 + - + -
123B GLY 3.6 0.5 + - - -
126B TYR* 3.3 19.7 - - + -
133B ILE* 4.2 8.5 - - + -
166B VAL* 5.1 5.4 - - + -
169B MET* 5.2 0.4 - - + -
170B CYS* 3.7 24.0 - - - -
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Residues in contact with MET 119 (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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115B MET 2.9 14.0 + - - +
116B ASN* 3.4 29.2 - - + +
118B ALA* 1.3 74.6 - - - +
120B GLU* 1.3 67.9 + - + +
126B TYR* 3.3 13.1 + - - +
133B ILE* 3.7 15.2 - - + +
137B TYR* 3.6 15.9 - - + +
395B ASN* 3.2 16.8 + - - -
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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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116B ASN* 2.8 18.7 + - - +
117B PHE* 3.2 39.6 - - - +
119B MET* 1.3 85.2 - - + +
121B ASN* 1.3 72.5 + - - +
178B LYS* 4.6 12.4 + - - -
393B SER* 5.5 0.2 - - - -
394B ASN* 4.1 4.8 + - + +
395B ASN* 3.2 27.7 + - - +
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Residues in contact with ASN 121 (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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117B PHE* 3.0 38.2 + - + +
118B ALA 3.3 0.2 + - - -
120B GLU* 1.3 94.2 + - - +
122B LEU* 1.3 64.9 + - + +
123B GLY 3.2 9.1 + - - -
124B ALA 4.1 0.3 + - - -
394B ASN* 2.5 41.0 + - - +
395B ASN* 3.3 18.1 - - - +
398B PHE* 3.8 16.7 - - + +
449B LYS* 5.1 0.3 - - - -
452B PHE* 3.3 27.2 - - + -
453B PHE* 5.4 2.0 - - + -
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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
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117B PHE* 4.5 11.2 - - + +
118B ALA* 2.9 30.6 + - + +
121B ASN* 1.3 84.1 - - + +
123B GLY* 1.3 51.0 + - - +
124B ALA 3.1 5.8 - - - -
125B LEU* 2.6 37.5 + - + +
126B TYR* 3.2 23.2 + - + -
169B MET* 3.8 38.8 - - + +
170B CYS* 4.2 11.7 - - - -
173B TYR* 3.6 35.9 - - + -
398B PHE* 5.2 4.7 - - + -
452B PHE* 5.1 3.1 - - + -
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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