Contacts of the helix formed by residues 115 - 127 (chain B) in PDB entry 2VF8
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 THR 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A ARG* 4.4 23.1 - - - +
111B GLY 3.2 4.9 - - - -
112B SER 2.7 21.2 + - - -
113B VAL 3.0 6.0 + - - +
114B THR* 1.3 75.4 + - - +
116B LEU* 1.3 66.7 + - - +
118B ASN* 3.1 22.3 + - - +
119B LEU* 3.5 22.8 + - - +
359B ARG* 4.2 12.1 + - - +
392B THR* 4.2 15.3 - - + -
395B TYR* 4.4 6.2 - - + -
396B SER* 6.0 1.6 - - - -
1847B SO4 5.3 0.7 + - - -
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Residues in contact with LEU 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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111B GLY 3.0 1.8 + - - -
114B THR* 3.0 32.6 + - - +
115B THR* 1.3 74.9 - - - +
117B SER* 1.3 69.9 + - - +
119B LEU* 2.7 20.7 + - + +
120B LEU* 3.1 12.6 + - + +
317B LEU* 3.9 14.8 - - + -
356B LEU* 4.1 14.8 - - + -
359B ARG* 3.6 38.6 - - + -
360B LEU* 3.7 38.8 - - + -
363B LEU* 5.0 4.3 - - + -
373B LEU* 4.4 12.1 - - + -
395B TYR* 4.0 2.0 - - - +
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Residues in contact with SER 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B SER* 4.5 4.0 + - - -
111B GLY* 2.8 38.9 + - - -
112B SER* 3.7 3.3 + - - -
116B LEU* 1.3 73.5 - - - +
118B ASN* 1.3 65.3 + - - +
119B LEU 2.8 0.5 + - - -
120B LEU* 2.8 19.6 + - - +
121B ARG* 3.1 20.7 + - - +
313B SER* 5.7 0.7 + - - -
373B LEU* 4.9 7.4 + - - +
1847B SO4 4.2 15.6 + - - -
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Residues in contact with ASN 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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78A ASN* 3.1 34.1 + - - +
115B THR* 3.1 10.3 + - - +
117B SER* 1.3 79.0 - - - +
119B LEU* 1.3 78.4 + - - +
120B LEU 3.2 0.5 + - - -
121B ARG* 3.1 35.6 + - - +
122B MET* 3.5 36.1 + - - +
139B ALA* 5.7 2.1 - - - +
1847B SO4 4.3 7.5 + - - +
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Residues in contact with LEU 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 THR* 3.5 18.9 + - - +
116B LEU* 2.7 24.0 + - - +
118B ASN* 1.3 89.4 - - - +
120B LEU* 1.3 58.8 + - - +
122B MET* 3.4 24.6 - - + +
123B LEU* 3.7 7.1 + - - +
352B MET* 4.9 9.1 - - + +
355B ASP* 3.9 22.7 - - + +
356B LEU* 3.6 32.0 - - + +
359B ARG* 4.5 18.8 - - - +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 3.1 15.2 + - + +
117B SER* 2.8 10.5 + - - +
119B LEU* 1.3 81.6 - - - +
121B ARG* 1.3 65.5 + - - +
122B MET 3.0 0.2 - - - -
123B LEU* 3.7 10.1 - - + +
124B TYR* 3.0 29.2 + - + -
309B ILE* 3.6 26.5 - - + +
312B LEU* 4.2 23.3 - - + -
313B SER* 4.9 7.0 - - - +
320B VAL* 5.0 11.9 - - + -
324B LEU* 5.4 3.1 - - + -
356B LEU* 4.3 23.1 - - + -
373B LEU* 5.4 13.2 - - + -
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Residues in contact with ARG 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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78A ASN* 4.7 1.8 + - - -
117B SER* 3.1 13.3 + - - +
118B ASN* 3.1 47.4 + - - +
120B LEU* 1.3 77.0 - - - +
122B MET* 1.3 54.6 + - - +
123B LEU 3.1 0.5 + - - -
124B TYR* 3.2 1.4 + - - +
125B SER* 2.8 35.3 + - - -
139B ALA* 3.5 32.6 - - + +
140B GLU* 5.0 2.7 - - - +
142B PHE* 3.2 32.4 + - + +
143B SER* 3.6 19.9 - - - -
145B ASN* 5.8 0.2 - - - +
309B ILE* 4.0 12.3 - - + -
1847B SO4 2.8 47.2 + - - -
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Residues in contact with MET 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 ASN* 3.5 30.7 + - - +
119B LEU* 3.4 24.2 - - + +
121B ARG* 1.3 79.4 - - - +
123B LEU* 1.3 58.7 + - - +
125B SER* 4.1 1.8 - - - -
126B ARG* 3.5 41.1 + - - +
139B ALA* 4.0 12.3 - - + -
351B ARG* 5.4 5.2 - - - +
352B MET* 3.4 31.9 - - + +
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Residues in contact with LEU 123 (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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119B LEU 3.7 2.8 + - - +
120B LEU* 3.2 19.0 + - + +
121B ARG 3.1 0.6 - - - -
122B MET* 1.3 75.8 - - - +
124B TYR* 1.3 70.2 + - + +
127B ALA* 2.8 41.2 + - + +
128B GLY 5.0 0.4 - - - +
304B PHE* 3.6 37.2 - - + -
324B LEU* 4.3 24.0 - - + -
349B LEU* 4.5 10.5 - - + -
352B MET* 3.8 21.3 - - + -
353B ALA* 4.4 14.1 - - - +
356B LEU* 4.3 13.9 - - + -
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Residues in contact with TYR 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 LEU* 3.0 28.1 + - + +
121B ARG 3.7 2.9 - - - +
123B LEU* 1.3 84.3 - - + +
125B SER* 1.3 56.9 + - - +
127B ALA 2.7 19.0 - - - +
128B GLY* 5.0 0.2 - - - -
130B TYR* 3.8 0.5 - - - -
142B PHE* 3.7 19.0 - + + -
302B VAL* 3.3 40.2 - - + +
303B THR 3.7 2.9 - - - -
304B PHE* 3.3 36.1 + + + +
307B LEU 2.9 18.0 + - - -
308B ASP 3.2 10.2 + - - -
309B ILE* 3.4 42.8 - - + -
312B LEU* 3.5 32.3 - - + +
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Residues in contact with SER 125 (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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121B ARG 2.8 20.7 + - - -
122B MET 4.5 0.2 - - - -
124B TYR* 1.3 77.7 - - - +
126B ARG* 1.3 85.3 + - - +
130B TYR* 3.2 22.7 + - - -
136B ILE* 4.4 7.7 - - - +
137B VAL 2.7 24.4 + - - -
138B TYR* 3.5 4.2 - - - -
139B ALA* 3.7 13.2 - - - -
142B PHE* 3.4 13.8 - - - -
1848B SO4 4.7 2.4 + - - -
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Residues in contact with ARG 126 (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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122B MET* 3.5 38.7 + - - +
125B SER* 1.3 94.0 + - - +
127B ALA* 1.3 60.4 + - - +
136B ILE* 5.5 5.1 - - + +
138B TYR* 3.3 33.1 - - - +
139B ALA* 3.4 34.1 - - - +
140B GLU* 4.8 3.4 + - - -
345B GLN* 4.5 13.3 - - - +
348B ALA* 5.2 8.0 - - + +
352B MET* 4.8 15.9 - - + -
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Residues in contact with ALA 127 (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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123B LEU* 2.8 18.9 + - + +
124B TYR 2.7 23.7 - - - +
125B SER 3.5 2.9 - - - +
126B ARG* 1.3 77.7 - - - +
128B GLY* 1.3 67.7 + - - +
130B TYR* 4.0 1.5 - - - -
338B ARG* 5.4 0.2 - - - +
345B GLN* 3.9 19.7 - - - +
348B ALA 5.7 0.4 - - - -
349B LEU* 4.3 33.0 - - + +
352B MET* 5.4 3.4 - - - -
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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