Contacts of the helix formed by residues 99 - 114 (chain B) in PDB entry 3GV5
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 LEU 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B TYR* 3.8 12.8 - - - +
59B GLN* 3.4 16.6 - - - +
96B GLY 3.3 23.6 - - - +
97B GLU 3.4 3.3 + - - +
98B ASP* 1.3 71.7 + - - +
100B THR* 1.3 55.6 + - - +
101B ARG 3.2 2.9 + - - -
102B TYR* 3.2 21.0 + - + -
103B ARG* 2.8 49.8 + - - +
125B PHE* 4.0 23.3 - - + -
422B GOL 4.6 1.2 + - - -
873P G 5.7 0.2 - - - +
841T C 3.4 35.4 - - - +
842T T 3.7 19.2 + - - +
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Residues in contact with THR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASP* 2.6 29.6 + - - -
99B LEU* 1.3 75.2 - - - +
101B ARG* 1.3 60.8 + - + +
103B ARG* 3.7 19.0 + - - +
104B GLU* 2.9 53.2 + - + +
331B ARG* 6.3 2.9 - - + -
334B GLN* 5.5 3.1 - - - +
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Residues in contact with ARG 101 (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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42B VAL* 4.2 16.2 - - + +
43B GLU* 3.0 42.4 + - - -
46B SER* 3.2 27.9 + - - +
95B ASN 4.4 9.3 + - - -
98B ASP* 4.5 13.5 + - - +
99B LEU 3.2 0.6 - - - -
100B THR* 1.3 77.4 - - + +
102B TYR* 1.3 70.3 + - + +
104B GLU* 3.5 11.0 + - - +
105B MSE 2.9 30.8 + - - +
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Residues in contact with TYR 102 (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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38B PHE* 3.4 12.6 - - + -
39B TYR* 3.5 74.0 - + + -
42B VAL* 3.8 24.0 - - + -
43B GLU* 2.5 31.5 + - - +
57B VAL* 3.5 8.3 - - - +
96B GLY* 3.4 33.5 - - - -
98B ASP 4.2 4.7 - - - -
99B LEU* 3.6 19.3 - - + +
101B ARG* 1.3 83.8 - - + +
103B ARG* 1.3 58.4 + - - +
105B MSE 3.3 0.3 + - - -
106B SER* 2.9 31.7 + - - -
125B PHE* 4.2 5.6 - - + -
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASP* 4.8 0.6 + - - -
99B LEU* 2.8 29.0 + - - +
100B THR* 3.7 34.5 + - - +
102B TYR* 1.3 71.9 - - - +
104B GLU* 1.3 66.5 + - + +
106B SER* 3.2 5.3 + - - -
107B TYR* 3.1 41.9 + - + -
125B PHE* 3.8 25.0 - - + -
299B PRO* 6.0 1.8 - - - -
304B GLU* 3.9 8.1 + - - -
331B ARG* 3.3 53.7 - - - +
842T T 3.3 29.1 + - - -
843T C 3.5 17.0 + - - -
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Residues in contact with GLU 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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100B THR* 2.9 41.7 + - + +
101B ARG* 3.9 10.3 - - - +
103B ARG* 1.3 79.5 - - + +
105B MSE 1.3 62.6 + - - +
107B TYR* 3.3 4.6 + - - +
108B LYS* 3.3 34.1 + - - +
334B GLN* 4.1 18.6 + - - +
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Residues in contact with MSE 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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38B PHE* 3.8 13.7 - - + -
42B VAL* 4.1 18.8 - - + -
45B ILE* 4.2 32.3 - - + -
101B ARG 2.9 17.3 + - - +
102B TYR 3.9 2.9 - - - +
104B GLU* 1.3 76.2 - - - +
106B SER* 1.3 63.8 + - - +
108B LYS* 3.1 29.1 + - - +
109B VAL* 3.0 20.3 + - - +
191B LEU* 4.2 20.2 - - - +
193B LEU* 3.4 31.6 - - + -
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Residues in contact with SER 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 5.8 0.2 - - - -
38B PHE* 3.7 6.8 - - - -
102B TYR 2.9 17.1 + - - -
103B ARG* 3.4 8.5 - - - -
105B MSE 1.3 76.6 - - - +
107B TYR* 1.3 61.6 - - - +
109B VAL* 3.2 9.0 + - - +
110B THR* 3.2 23.6 + - - +
122B ARG* 2.8 33.7 + - - -
125B PHE* 2.6 36.8 + - - +
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Residues in contact with TYR 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 ARG* 3.1 35.2 + - + +
104B GLU* 4.1 4.5 - - - +
105B MSE 3.3 0.4 - - - -
106B SER* 1.3 73.8 - - - +
108B LYS* 1.3 60.0 + - - +
110B THR* 3.5 5.8 + - + -
111B GLU* 3.0 54.4 + - + +
122B ARG* 3.3 49.1 + - - +
125B PHE* 5.6 2.0 - + - -
297B GLY 3.7 16.0 + - - -
298B PRO* 4.4 4.5 - - + -
299B PRO* 3.2 42.3 - - + +
843T C 5.3 5.9 + - - -
844T A 5.3 0.9 + - - -
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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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104B GLU* 3.3 23.0 + - - +
105B MSE 3.1 27.2 + - - +
107B TYR* 1.3 77.8 - - - +
109B VAL* 1.3 55.1 - - - +
111B GLU* 3.5 9.0 + - - +
112B LEU* 2.9 30.3 + - - +
191B LEU* 3.9 32.8 - - + +
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Residues in contact with VAL 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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33B VAL* 5.5 0.9 - - + -
35B LEU* 4.0 23.3 - - + -
105B MSE 3.0 14.1 + - - +
106B SER* 3.2 9.2 + - - +
108B LYS* 1.3 72.8 - - - +
110B THR* 1.3 66.9 + - - +
112B LEU* 3.2 5.8 + - - +
113B LEU* 3.1 31.0 + - + +
125B PHE 6.1 0.2 - - - +
128B ASN* 3.7 20.4 - - - +
187B MSE 4.5 19.1 - - + -
191B LEU* 3.8 12.3 - - + -
193B LEU* 3.3 34.1 - - + -
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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 SER 3.2 5.9 + - - +
107B TYR* 3.5 6.7 + - + -
109B VAL* 1.3 76.1 - - - +
111B GLU* 1.3 58.9 + - - +
113B LEU* 3.2 6.5 + - - +
114B GLU* 2.9 42.9 + - - +
120B VAL* 4.1 7.9 + - - +
122B ARG* 2.8 49.2 - - + +
128B ASN* 2.9 36.1 - - - +
297B GLY 6.0 0.2 + - - -
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B TYR* 3.0 42.5 + - + +
108B LYS* 4.0 8.7 - - - +
110B THR* 1.3 75.4 - - - +
112B LEU* 1.3 65.7 + - - +
114B GLU* 3.4 30.9 + - - +
115B GLU* 3.5 14.7 + - - +
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Residues in contact with LEU 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 17.6 + - - +
109B VAL* 3.2 6.5 + - - +
111B GLU* 1.3 77.5 - - - +
113B LEU* 1.3 67.4 + - + +
115B GLU* 3.1 39.3 + - - +
116B PHE* 3.7 13.0 - - + -
183B MSE 4.2 2.5 - - - +
186B ALA* 3.8 22.7 - - + +
187B MSE 3.7 31.6 - - + +
190B GLN* 3.2 39.9 - - + +
191B LEU* 4.8 8.1 - - + -
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Residues in contact with LEU 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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33B VAL* 4.2 18.8 - - + -
109B VAL* 3.1 22.6 + - + +
110B THR 3.5 7.6 - - - +
112B LEU* 1.3 81.0 - - + +
114B GLU* 1.3 56.3 + - - +
115B GLU 3.0 5.6 - - - -
116B PHE* 2.9 30.0 + - - +
117B SER 3.4 5.0 + - - +
120B VAL* 4.0 13.8 - - + +
128B ASN* 3.5 40.8 - - + +
130B VAL* 4.5 8.1 - - + -
183B MSE 3.8 42.7 - - + +
187B MSE 4.6 7.2 - - - -
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Residues in contact with GLU 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 THR* 2.9 31.2 + - - +
111B GLU* 3.6 28.6 - - - +
112B LEU 3.2 0.6 - - - -
113B LEU* 1.3 75.0 - - - +
115B GLU* 1.3 60.1 + - - +
116B PHE 3.2 0.2 - - - -
117B SER 3.1 22.7 - - - +
118B PRO* 4.2 11.5 - - + +
120B VAL* 3.7 17.4 - - + +
295B LEU* 3.6 23.0 - - - +
297B GLY* 4.9 7.3 + - - -
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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