Contacts of the helix formed by residues 106 - 121 (chain B) in PDB entry 1XGS
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 GLU 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B ASP* 1.3 80.5 - - - +
107B LEU* 1.3 65.3 + - - +
109B GLU* 3.7 21.6 - - - +
110B ALA* 3.0 19.8 + - - +
142B ARG* 6.0 0.9 - - + -
144B PHE* 3.4 24.6 - - + -
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Residues in contact with LEU 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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78B TYR* 4.4 8.1 - - + +
105B ASP* 3.3 12.9 + - - +
106B GLU* 1.3 79.0 - - - +
108B MET* 1.3 62.9 + - - +
110B ALA* 3.4 8.0 + - - +
111B ALA* 3.5 9.2 + - - +
144B PHE* 3.6 40.7 - - + -
190B ALA* 3.7 28.8 - - + +
191B THR* 3.8 4.7 - - - +
192B ILE* 4.5 9.2 - - + -
275B ILE* 3.5 44.4 - - + +
277B ALA* 3.7 17.0 - - + +
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Residues in contact with MET 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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78B TYR* 4.1 13.2 - - + -
97B THR* 3.2 47.1 - - + +
98B VAL* 4.1 0.9 - - - -
99B ARG* 3.9 29.2 - - + +
104B GLU* 3.4 34.8 - - + +
105B ASP* 3.1 31.0 + - - +
107B LEU* 1.3 74.2 - - - +
109B GLU* 1.3 64.7 + - - +
111B ALA* 3.3 2.3 + - - +
112B LYS* 3.1 19.1 + - - +
277B ALA* 4.1 9.6 - - + -
279B PHE* 3.3 17.0 - - + -
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Residues in contact with GLU 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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104B GLU* 4.4 9.1 + - + +
105B ASP 2.9 15.9 + - - +
106B GLU* 3.7 20.8 - - - +
107B LEU 3.4 0.2 - - - -
108B MET* 1.3 77.0 - - - +
110B ALA* 1.3 55.5 + - - +
112B LYS* 3.9 5.9 - - - +
113B GLU* 2.8 38.4 + - + +
142B ARG* 2.8 34.7 + - - +
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Residues in contact with ALA 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 GLU 3.0 14.8 + - - +
107B LEU 3.7 6.3 - - - +
108B MET 3.2 0.4 - - - -
109B GLU* 1.3 76.5 - - - +
111B ALA* 1.3 57.9 + - - +
113B GLU* 3.8 0.7 - - - +
114B ALA* 2.9 31.1 + - - +
138B GLU* 4.5 2.6 - - - +
139B ILE* 4.0 17.5 - - + +
142B ARG* 3.5 29.8 - - + +
144B PHE* 3.7 17.5 - - + -
190B ALA* 4.7 2.7 - - + -
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU 3.5 7.1 + - - +
108B MET 3.3 4.7 + - - +
110B ALA* 1.3 78.7 - - - +
112B LYS* 1.3 62.5 + - - +
114B ALA* 3.4 6.9 + - - +
115B LEU* 3.1 22.7 + - - +
139B ILE* 4.8 0.4 - - - -
188B PRO* 3.9 20.0 - - - +
190B ALA* 4.3 10.2 - - + +
277B ALA* 4.0 25.1 - - + +
279B PHE* 3.7 21.2 - - + +
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Residues in contact with LYS 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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96B VAL* 5.8 0.8 - - - +
104B GLU* 2.6 39.8 + - - +
108B MET 3.1 14.8 + - - +
109B GLU* 3.9 5.2 - - - +
111B ALA* 1.3 73.4 - - - +
113B GLU* 1.3 67.4 + - + +
115B LEU* 3.2 8.2 + - + +
116B ASN* 3.0 36.8 + - - +
279B PHE* 3.4 37.5 - - + -
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Residues in contact with GLU 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 GLU* 2.8 26.9 + - + +
110B ALA 4.0 0.7 - - - +
112B LYS* 1.3 76.1 - - + +
114B ALA* 1.3 62.3 + - - +
116B ASN* 3.0 28.1 + - - +
117B ALA* 2.8 31.5 + - - +
138B GLU* 3.9 9.7 - - - +
142B ARG* 3.4 34.3 + - - +
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Residues in contact with ALA 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 ALA 2.9 19.9 + - - +
111B ALA 3.5 6.1 - - - +
113B GLU* 1.3 75.6 - - - +
115B LEU* 1.3 62.6 + - - +
117B ALA* 3.4 2.9 + - - +
118B ALA 3.1 17.8 + - - -
135B ILE* 3.7 33.4 - - + +
138B GLU* 3.7 12.5 - - + +
139B ILE* 3.8 11.9 - - + -
188B PRO* 3.8 15.5 - - + -
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Residues in contact with LEU 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 ALA 3.1 12.8 + - - +
112B LYS* 3.4 11.7 - - + +
114B ALA* 1.3 74.7 - - - +
116B ASN* 1.3 68.0 + - - +
118B ALA* 3.2 3.8 + - - +
119B ILE* 3.1 43.5 + - + +
186B ILE* 3.6 39.9 - - + +
188B PRO* 3.7 12.5 - - + +
279B PHE* 3.8 11.2 - - + -
280B GLU* 3.7 23.1 - - - +
281B HIS* 3.6 30.1 - - + +
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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 LYS* 3.0 27.8 + - - +
113B GLU* 3.0 35.4 + - - +
115B LEU* 1.3 81.6 - - - +
117B ALA* 1.3 60.8 + - - +
119B ILE* 3.4 10.5 + - - +
120B SER* 2.9 30.4 + - - +
281B HIS* 5.8 1.7 - - - -
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Residues in contact with ALA 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 GLU* 2.8 18.5 + - - +
114B ALA 3.6 3.8 - - - +
116B ASN* 1.3 78.3 - - - +
118B ALA* 1.3 61.0 + - - +
120B SER* 3.5 13.7 + - - -
121B VAL* 3.5 18.2 + - - +
134B ALA* 4.0 14.5 - - + +
138B GLU* 3.5 27.6 - - + +
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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 ALA 3.1 9.5 + - - +
115B LEU 3.2 4.0 + - - +
117B ALA* 1.3 74.1 - - - +
119B ILE* 1.3 65.5 + - - +
121B VAL* 3.4 7.8 + - - +
122B ALA* 3.2 23.4 + - - +
131B LEU* 3.8 14.8 - - + +
134B ALA* 4.2 7.6 - - - +
135B ILE* 3.6 34.8 - - + -
186B ILE* 3.9 15.9 - - + -
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Residues in contact with ILE 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 LEU* 3.1 29.9 + - + +
116B ASN* 3.8 11.2 - - - +
118B ALA* 1.3 75.4 - - - +
120B SER* 1.3 63.4 + - - +
122B ALA* 3.3 22.9 + - - +
186B ILE* 4.3 16.4 - - + -
281B HIS* 4.0 31.4 - - + -
283B ILE* 4.4 6.1 - - + -
290B VAL* 3.9 22.0 - - + +
292B VAL* 4.0 21.5 - - + -
295B GLU* 5.6 2.7 - - - +
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Residues in contact with SER 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ASN* 2.9 19.7 + - - +
117B ALA* 3.6 9.1 - - - -
118B ALA 3.2 0.2 - - - -
119B ILE* 1.3 78.7 - - - +
121B VAL* 1.3 61.1 + - - +
122B ALA 4.8 1.7 - - - +
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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
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117B ALA 3.5 14.3 + - - +
118B ALA* 3.4 10.9 + - - +
119B ILE 3.3 0.2 - - - -
120B SER* 1.3 81.9 - - - +
122B ALA* 1.3 64.7 + - - +
123B ARG* 3.9 4.2 + - - +
126B VAL* 3.4 21.1 - - + +
130B GLU* 4.0 22.7 - - + +
131B LEU* 3.8 21.3 - - + -
134B ALA* 4.5 7.0 - - + -
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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
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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