Contacts of the helix formed by residues 107 - 124 (chain B) in PDB entry 1GXD
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 ASP 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B LEU* 1.3 76.0 - - - +
108B PRO* 1.3 75.2 - - + +
109B GLU* 2.7 36.4 + - - +
110B THR* 2.6 41.6 + - - -
111B VAL* 3.1 9.0 + - - +
191B VAL* 5.9 0.5 - - - +
193B ARG* 3.1 30.7 + - + +
203B TYR* 4.4 1.0 - - - -
304B PRO* 4.0 9.0 - - + -
305B GLU* 3.8 25.0 + - + +
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Residues in contact with PRO 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TYR* 4.3 19.3 - - + +
106B LEU 3.7 0.4 - - - -
107B ASP* 1.3 86.5 - - + +
109B GLU* 1.3 66.7 + - - +
112B ASP* 3.0 32.7 + - - +
285B TYR* 3.9 35.7 - - + +
304B PRO* 3.7 32.3 - - + +
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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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107B ASP* 2.7 20.3 + - - +
108B PRO* 1.3 74.5 - - - +
110B THR* 1.3 59.5 + - - +
112B ASP* 3.9 4.7 - - - +
113B ASP* 3.1 24.3 + - - +
193B ARG* 2.8 38.0 + - - +
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Residues in contact with THR 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 LEU* 3.6 30.7 - - + -
107B ASP* 2.6 29.8 + - - -
109B GLU* 1.3 73.4 - - - +
111B VAL* 1.3 68.5 + - - +
113B ASP* 3.0 7.2 + - - +
114B ALA* 2.7 22.2 + - + +
117B ARG* 5.5 1.3 + - - +
186B LEU* 4.1 20.9 - - + -
193B ARG* 4.8 1.0 - - - -
203B TYR* 2.5 33.7 + - + +
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TYR* 3.3 34.8 - - + -
103B THR* 4.1 16.4 - - + +
106B LEU* 3.7 33.4 - - + +
107B ASP 3.1 2.5 + - - +
108B PRO 4.0 1.6 - - - +
110B THR* 1.3 75.7 - - - +
112B ASP* 1.3 70.3 + - - +
114B ALA* 2.9 16.9 + - - +
115B PHE* 2.9 40.6 + - + -
144B PHE* 4.5 3.8 - - + -
368B LEU* 4.2 10.1 - - + -
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Residues in contact with ASP 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TYR* 5.4 1.0 + - - -
99B ILE* 3.1 11.8 - - - +
102B TYR* 2.8 33.3 + - - -
108B PRO* 3.0 17.7 + - - +
109B GLU* 3.9 5.3 - - - +
111B VAL* 1.3 76.0 - - - +
113B ASP* 1.3 67.3 + - - +
115B PHE* 2.8 11.8 + - - +
116B ALA* 2.9 12.7 + - - +
132B ARG* 2.5 41.7 + - - +
285B TYR* 4.4 5.5 + - - -
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Residues in contact with ASP 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 3.1 15.7 + - - +
110B THR* 3.0 5.9 + - - +
112B ASP* 1.3 78.3 - - - +
114B ALA* 1.3 64.3 + - - +
116B ALA* 2.9 10.3 + - - +
117B ARG* 2.9 56.3 + - - +
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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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106B LEU* 6.0 0.2 - - + -
110B THR* 2.7 17.4 + - + +
111B VAL* 3.3 13.0 - - - +
113B ASP* 1.3 73.0 + - - +
115B PHE* 1.3 63.5 + - - +
117B ARG* 3.5 20.9 + - - +
118B ALA* 3.2 19.9 + - - +
186B LEU* 4.7 10.5 - - + -
368B LEU* 4.5 13.5 - - + -
369B PHE* 3.9 27.2 - - - +
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Residues in contact with PHE 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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97B TYR* 4.7 5.8 - - + -
99B ILE* 3.6 36.8 - - + -
111B VAL* 2.9 29.3 + - + -
112B ASP* 2.8 7.4 + - - +
114B ALA* 1.3 74.5 - - - +
116B ALA* 1.3 68.0 + - - +
118B ALA* 2.8 16.7 + - - +
119B PHE* 3.2 14.1 + - - -
142B ILE* 3.4 36.3 - - + -
144B PHE* 3.8 20.0 - + - -
178B PHE* 3.6 28.0 - + - -
368B LEU* 4.2 11.4 - - + -
372B ALA* 4.0 10.8 - - + -
376B PHE* 4.0 14.1 - + + -
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Residues in contact with ALA 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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97B TYR* 4.4 15.1 + - - +
112B ASP 2.9 10.9 + - - +
113B ASP* 3.4 13.7 - - - +
115B PHE* 1.3 78.8 - - - +
117B ARG* 1.3 64.3 + - + +
119B PHE* 3.1 16.8 + - - +
120B GLN* 3.1 12.3 + - - +
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Residues in contact with ARG 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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110B THR* 6.1 0.8 - - - +
113B ASP* 2.9 44.8 + - - +
114B ALA* 3.8 14.2 - - - +
116B ALA* 1.3 76.9 - - + +
118B ALA* 1.3 60.5 + - - +
120B GLN* 3.3 20.9 + - - +
121B VAL* 3.2 22.5 + - - +
186B LEU* 4.8 17.8 - - - +
369B PHE* 3.3 52.4 - - + +
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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 3.2 12.8 + - - +
115B PHE 2.8 17.5 + - - +
117B ARG* 1.3 68.4 - - - +
119B PHE* 1.3 64.4 + - - +
121B VAL* 3.1 25.9 + - - +
122B TRP* 3.7 10.6 + - - -
369B PHE* 4.0 6.2 - - - +
372B ALA* 3.8 7.6 - - + -
373B ALA* 3.8 23.4 - - - +
376B PHE* 3.7 22.0 - - + -
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Residues in contact with PHE 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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97B TYR* 3.1 68.2 - + + -
115B PHE 3.2 8.0 + - - -
116B ALA* 3.1 9.4 + - - +
118B ALA* 1.3 75.9 - - - +
120B GLN* 1.3 68.6 + - - +
122B TRP* 2.9 12.6 + - - -
123B SER* 3.0 11.3 + - - -
130B PHE* 3.1 57.4 - + + -
140B ILE* 3.9 9.2 - - + -
376B PHE* 3.1 46.2 - + + -
380B MET* 3.7 7.9 - - + -
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Residues in contact with GLN 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 ALA 3.1 9.4 + - - +
117B ARG* 3.3 26.5 - - - +
118B ALA 3.2 0.2 - - - -
119B PHE* 1.3 75.7 - - - +
121B VAL* 1.3 66.0 + - - +
122B TRP 2.8 1.7 + - - -
123B SER* 3.1 7.4 + - - +
124B ASP* 3.1 53.9 + - - +
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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
----------------------------------------------------------
117B ARG 3.3 15.7 - - - +
118B ALA* 3.1 14.4 - - - +
119B PHE 3.0 0.8 - - - -
120B GLN* 1.3 78.3 - - - +
122B TRP* 1.3 63.4 + - + +
124B ASP* 4.3 8.7 - - - +
125B VAL* 4.0 4.0 - - - +
369B PHE* 3.7 24.7 - - + -
373B ALA* 4.1 8.1 - - + -
391B LEU* 4.3 7.2 - - + -
402B PHE* 3.7 19.1 - - + -
404B LEU* 3.5 41.8 - - + +
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Residues in contact with TRP 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 ALA 3.7 14.5 + - - -
119B PHE* 2.9 8.0 + - - +
120B GLN 2.8 0.2 + - - -
121B VAL* 1.3 82.5 - - + +
123B SER* 1.3 61.7 + - - +
125B VAL* 3.2 12.2 + - - +
126B THR* 2.6 24.0 + - - +
128B LEU* 4.6 10.1 - - + -
130B PHE* 4.4 11.2 - - + -
373B ALA* 3.1 25.7 + - - +
376B PHE* 4.3 11.0 - - + -
377B GLY* 3.4 31.0 - - - +
380B MET* 4.8 6.5 - - + -
382B LEU* 3.5 18.2 - - + -
391B LEU* 4.2 12.3 - - + -
392B MET* 4.3 7.2 - - + -
404B LEU* 3.7 32.3 - - + -
408B ASP* 3.9 11.7 - - + -
412B ILE* 3.6 39.5 - - + -
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PHE 3.0 13.4 + - - -
120B GLN* 3.9 10.3 - - - -
122B TRP* 1.3 71.6 - - - +
124B ASP* 1.3 54.7 - - - +
125B VAL 2.1 22.7 + - - -
126B THR* 2.4 28.5 + - - +
128B LEU* 3.2 24.0 + - - -
129B ARG* 4.6 2.4 - - - -
130B PHE* 3.5 16.8 + - - -
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Residues in contact with ASP 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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120B GLN* 3.1 47.2 + - - +
121B VAL* 4.3 8.2 - - - +
123B SER* 1.3 76.4 - - - +
125B VAL* 1.3 64.9 + - + +
126B THR 3.7 0.4 - - - -
418B ALA 4.8 1.0 - - - +
419B SER* 5.8 0.9 - - - -
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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