Contacts of the helix formed by residues 86 - 99 (chain B) in PDB entry 1V2E
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 GLY 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B THR* 2.7 28.9 + - - -
85B SER* 1.3 72.5 - - - +
87B ALA* 1.3 66.8 + - - -
88B THR 3.2 2.5 - - - -
89B GLU 3.1 9.5 + - - -
90B ALA 3.4 0.3 + - - -
230B ARG* 3.2 15.9 + - - -
231B VAL 3.8 3.4 - - - -
232B GLY* 3.3 10.9 - - - +
1510B PLP 3.4 15.9 - - - -
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B THR* 4.5 0.4 - - - -
86B GLY* 1.3 69.4 - - - -
88B THR* 1.3 57.3 + - - +
90B ALA* 2.5 37.4 + - - +
91B LEU* 2.9 10.5 + - + +
193B VAL* 3.5 26.5 - - + -
217B VAL* 3.7 13.7 - - + -
218B GLY 3.7 7.6 - - - +
232B GLY* 4.0 2.2 - - - -
1510B PLP 2.7 34.4 + - + +
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Residues in contact with THR 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A GLN 4.0 5.8 - - - +
250A TRP* 3.3 24.1 - - - +
252A SER* 3.8 19.5 - - - -
253A PHE* 4.0 10.8 - - + +
87B ALA* 1.3 76.0 - - - +
89B GLU* 1.3 60.9 + - - +
91B LEU* 3.6 10.4 + - - +
92B TYR* 3.1 21.8 + - - +
112B PHE* 5.2 0.5 - - - -
114B VAL* 4.6 19.7 - - + +
230B ARG* 4.1 11.3 + - - -
1510B PLP 2.8 29.6 + - - -
1520B KMT 5.7 2.4 - - - +
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Residues in contact with GLU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 5.5 0.3 - - - +
251A THR* 3.0 21.2 + - - +
252A SER* 4.3 2.4 - - - -
84B THR* 3.7 5.6 - - - +
85B SER* 2.8 39.5 + - - +
86B GLY 3.1 10.5 + - - +
87B ALA 3.0 0.6 - - - -
88B THR* 1.3 78.2 - - - +
90B ALA* 1.3 67.9 + - - +
92B TYR* 4.4 1.8 - - + -
93B VAL* 3.1 33.0 + - + +
248B ARG* 3.2 20.8 + - - -
251B THR* 2.6 29.3 + - + +
252B SER* 2.7 22.2 + - - -
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B THR* 3.8 11.2 + - - +
86B GLY 3.4 2.6 + - - -
87B ALA* 2.5 23.3 + - - +
89B GLU* 1.3 74.8 - - - +
91B LEU* 1.3 50.0 + - - +
93B VAL* 3.8 1.6 - - - +
94B LEU* 2.8 39.2 + - - +
217B VAL* 3.5 33.4 - - + -
233B TRP 4.4 1.6 - - - +
234B ILE* 3.6 25.0 - - + +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ALA* 2.9 11.4 + - + +
88B THR* 3.8 7.9 - - - +
90B ALA* 1.3 71.8 - - - +
92B TYR* 1.3 71.1 + - - +
94B LEU* 3.0 5.9 + - - +
95B LEU* 3.0 27.6 + - + +
114B VAL* 4.5 11.9 - - + -
115B TYR* 3.7 26.2 - - + -
118B ASP* 4.1 13.5 - - - +
157B LEU* 5.0 5.6 - - + -
189B ILE* 4.4 22.2 - - + -
191B ASP* 3.3 33.4 - - + +
217B VAL* 4.6 11.0 - - + -
1510B PLP 4.2 14.1 - - + -
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Residues in contact with TYR 92 (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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92A TYR* 2.2 46.3 + + - -
96A GLN* 3.2 17.5 + - - -
250A TRP* 3.5 29.8 - - + +
251A THR* 4.0 21.1 - - + +
88B THR 3.1 9.3 + - - +
89B GLU* 4.0 3.1 - - + +
91B LEU* 1.3 81.1 - - - +
93B VAL* 1.3 73.3 + - + +
95B LEU* 3.4 1.7 + - - +
96B GLN* 3.0 50.6 + - + +
118B ASP* 3.2 29.3 + - + +
121B LEU* 4.3 21.5 - - + -
251B THR* 4.3 8.7 - - + -
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B THR* 5.7 0.9 - - + -
89B GLU* 3.1 33.7 + - + +
90B ALA* 3.8 3.1 - - - +
92B TYR* 1.3 84.7 - - + +
94B LEU* 1.3 57.9 + - - +
96B GLN* 3.3 7.2 + - - +
97B SER* 2.7 34.5 + - - +
234B ILE* 5.0 7.0 - - + -
244B LEU* 3.8 21.5 - - + +
247B MET* 3.4 27.3 - - + +
248B ARG* 3.8 21.5 - - + +
251B THR* 4.3 6.7 - - + +
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ALA 2.8 19.6 + - - +
91B LEU* 3.0 8.0 + - - +
93B VAL* 1.3 68.8 - - - +
95B LEU* 1.3 57.8 + - - +
96B GLN 3.0 0.9 - - - -
97B SER* 2.7 28.0 + - - -
98B LEU* 3.2 19.2 + - + +
189B ILE* 3.8 31.9 - - + -
215B PHE* 4.3 22.2 - - + -
217B VAL* 3.5 32.1 - - + -
234B ILE* 3.7 16.6 - - + -
244B LEU* 3.5 32.3 - - + -
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 3.0 17.5 + - + +
92B TYR 4.1 2.0 - - - +
94B LEU* 1.3 75.4 - - - +
96B GLN* 1.3 61.9 + - - +
97B SER 3.1 0.7 + - - -
98B LEU* 4.7 2.9 - - + +
99B VAL* 3.2 34.6 + - + +
105B VAL* 4.2 27.4 - - + -
115B TYR* 3.8 9.4 - - + +
118B ASP* 3.3 40.2 - - + +
119B ALA* 3.8 12.3 - - + +
122B ALA* 3.7 3.1 - - + +
155B ALA* 6.2 0.2 - - + -
157B LEU* 4.0 22.7 - - + -
189B ILE* 3.7 25.6 - - + -
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Residues in contact with GLN 96 (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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4A HIS* 4.9 0.3 - - - +
6A ARG* 2.9 53.0 + - - +
7A THR* 4.6 0.9 - - - +
92A TYR* 4.0 6.4 + - - +
96A GLN* 4.2 6.5 - - - +
121A LEU* 5.0 6.3 + - - +
92B TYR* 3.0 54.1 + - + +
93B VAL* 3.5 9.2 - - - +
94B LEU 3.0 0.8 - - - -
95B LEU* 1.3 76.6 - - - +
97B SER* 1.3 58.2 + - - +
99B VAL 4.6 0.2 - - - -
118B ASP* 4.3 3.3 - - - +
121B LEU 3.6 19.3 + - - +
122B ALA* 3.7 19.7 + - - +
247B MET* 3.7 17.9 - - + +
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Residues in contact with SER 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 3.8 6.7 - - - +
4A HIS* 2.9 26.0 + - - +
7A THR* 3.5 18.5 - - - +
93B VAL 2.7 17.4 + - - -
94B LEU 2.7 17.8 + - - -
96B GLN* 1.3 74.3 - - - +
98B LEU* 1.3 62.7 + - - +
244B LEU* 3.5 25.5 - - - +
247B MET* 3.4 22.2 - - - +
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Residues in contact with LEU 98 (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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2A ARG 5.2 2.6 - - - +
3A LEU* 4.0 14.4 - - + -
4A HIS* 4.2 9.5 + - - +
94B LEU* 3.2 17.5 + - + +
95B LEU* 4.8 2.0 - - + +
97B SER* 1.3 88.2 - - - +
99B VAL* 1.3 71.5 + - + +
103B ASP* 3.8 6.8 - - - +
154B ARG* 4.2 10.4 - - - +
155B ALA* 4.6 3.4 - - + -
187B PHE* 4.0 42.4 - - + -
189B ILE* 3.7 36.6 - - + -
215B PHE* 3.8 28.0 - - + -
244B LEU* 5.5 1.6 - - + -
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A HIS* 3.6 5.8 - - - +
6A ARG* 2.8 17.4 + - - -
95B LEU* 3.2 23.8 + - + +
97B SER 3.7 1.4 - - - -
98B LEU* 1.3 92.6 - - + +
100B GLY* 1.3 58.3 + - - +
103B ASP* 3.4 14.8 - - + -
105B VAL* 3.3 35.7 - - + -
119B ALA* 5.3 2.2 - - - +
122B ALA* 3.4 16.7 - - + +
124B ALA* 3.8 9.4 - - + -
154B ARG* 3.8 18.2 - - + -
155B ALA* 5.0 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
------------------------------------------------------------
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