Contacts of the helix formed by residues 278 - 289 (chain B) in PDB entry 2VGZ
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 LYS 278 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B PRO* 4.2 27.7 - - + +
108B GLN* 2.8 43.0 + - - +
109B MET 5.9 0.2 - - - +
110B ASP* 3.7 34.5 - - + +
276B GLY 3.4 0.6 + - - -
277B PRO* 1.3 70.1 - - - +
279B PRO* 1.3 69.4 - - + +
281B ILE* 3.5 1.1 + - - +
282B GLU* 3.0 26.3 + - + +
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Residues in contact with PRO 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-3B MET 3.7 27.1 - - - +
-2B LEU* 3.7 18.6 - - + +
3B TYR* 3.7 21.5 - - + -
104B PRO* 3.3 26.2 - - + +
105B SER* 4.6 0.4 - - - -
107B GLY* 4.4 0.2 - - - -
277B PRO* 3.3 13.9 - - + +
278B LYS* 1.3 90.4 - - + +
280B LEU* 1.3 57.7 + - - +
282B GLU* 3.8 9.3 - - + +
283B ARG* 3.4 29.6 + - - +
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2B LEU* 4.7 0.4 - - + -
3B TYR* 3.7 46.4 - - + +
6B PHE* 5.2 1.6 - - + -
7B ILE* 3.4 35.4 - - + -
127B MET* 3.6 16.9 - - + +
226B LEU* 4.0 14.6 - - + -
256B ILE* 3.7 29.2 - - + -
277B PRO* 2.9 21.2 + - + +
279B PRO* 1.3 75.6 - - - +
281B ILE* 1.3 66.1 + - + +
282B GLU 3.2 1.3 - - - -
283B ARG* 3.2 5.2 + - - +
284B VAL* 3.1 21.1 + - - +
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Residues in contact with ILE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASP* 3.8 26.2 - - + +
111B LEU 4.3 2.2 - - - +
112B CYS* 3.9 16.2 - - + -
256B ILE* 5.4 4.5 - - + -
274B LEU* 4.0 31.4 - - + +
275B THR 4.1 5.6 - - - -
276B GLY* 3.7 32.1 - - - +
277B PRO 3.1 11.8 + - - +
278B LYS 3.8 5.8 - - - +
280B LEU* 1.3 77.1 - - + +
282B GLU* 1.3 55.8 + - - +
284B VAL* 3.1 6.5 + - + +
285B ILE* 2.8 45.7 + - + +
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Residues in contact with GLU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-3B MET* 6.1 0.5 - - - +
-2B LEU* 5.1 3.8 - - - +
16B PRO* 6.4 0.9 - - - -
110B ASP* 5.4 0.4 + - - -
278B LYS* 3.0 21.6 + - + +
279B PRO* 3.8 8.6 - - + +
280B LEU 3.2 0.2 - - - -
281B ILE* 1.3 73.4 - - - +
283B ARG* 1.3 94.1 + - - +
285B ILE* 3.3 12.3 + - + +
286B LEU* 2.9 42.8 + - + +
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Residues in contact with ARG 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2B LEU* 3.8 33.9 - - + +
7B ILE* 4.4 6.7 - - + -
11B SER* 2.7 49.8 + - - +
12B ALA 3.2 10.7 + - - -
14B ARG* 2.8 33.2 + - - +
127B MET* 3.6 15.3 - - - -
279B PRO 3.4 16.7 + - - +
280B LEU 3.2 8.6 + - - +
282B GLU* 1.3 99.8 + - - +
284B VAL* 1.3 61.2 + - - +
286B LEU* 3.4 21.9 + - - +
287B HIS* 3.2 21.1 + - - +
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Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B CYS* 4.7 5.4 - - - -
114B THR* 5.0 2.7 - - + -
120B GLY* 5.0 0.9 - - - +
123B LYS* 4.2 16.6 - - + +
124B VAL* 3.9 25.6 - - + +
127B MET* 4.3 11.7 - - + -
274B LEU* 3.7 33.9 - - + -
280B LEU 3.1 17.8 + - - +
281B ILE 3.1 7.8 + - - +
283B ARG* 1.3 75.3 - - - +
285B ILE* 1.4 57.9 + - - +
287B HIS* 3.1 9.8 + - - +
288B ILE* 2.9 42.9 + - + +
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Residues in contact with ILE 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B SER* 3.9 24.9 - - - -
78B ALA* 4.0 20.9 - - + +
110B ASP* 4.6 7.2 - - - +
111B LEU 5.1 0.7 - - - +
112B CYS* 3.5 22.9 - - + -
281B ILE* 2.8 41.4 + - + +
282B GLU* 3.8 10.3 - - + +
284B VAL* 1.4 71.9 - - - +
286B LEU* 1.3 60.0 + - + +
288B ILE* 3.2 9.3 + - + +
289B GLN* 2.8 38.7 + - - +
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Residues in contact with LEU 286 (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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14B ARG* 3.6 38.0 - - + +
15B ASN* 4.1 9.4 - - - +
16B PRO* 3.7 24.9 - - + -
17B SER* 5.5 0.2 - - - -
282B GLU* 2.9 30.5 + - + +
283B ARG* 3.5 37.7 - - - +
285B ILE* 1.3 79.1 - - + +
287B HIS* 1.3 62.2 + - - +
289B GLN* 3.4 37.5 + - - +
290B VAL* 3.9 11.6 + - - +
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Residues in contact with HIS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A CYS* 4.6 2.9 - - - -
126A GLU* 3.0 23.7 + - - -
14B ARG* 3.3 42.1 + - - +
123B LYS* 3.3 35.4 + - + +
126B GLU* 3.4 31.7 + - + +
127B MET 5.8 0.6 + - - -
283B ARG 3.2 9.8 + - - +
284B VAL* 3.1 11.7 + - - +
286B LEU* 1.3 74.8 - - - +
288B ILE* 1.3 66.1 + - - +
290B VAL* 3.1 19.0 + - + +
291B SER* 3.1 15.4 + - - -
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Residues in contact with ILE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B SER* 4.1 13.2 - - - +
112B CYS* 3.9 28.0 - - - -
113B VAL 4.6 4.3 - - - +
114B THR* 4.1 14.1 - - + -
119B GLN* 4.2 10.1 - - - +
123B LYS* 3.6 20.2 - - + +
284B VAL* 2.9 28.4 + - + +
285B ILE* 3.6 8.1 - - - +
287B HIS* 1.3 75.9 - - - +
289B GLN* 1.3 62.9 + - - +
291B SER* 3.0 12.5 + - - -
292B THR* 3.4 15.8 + - - +
293B LEU 3.0 44.2 + - - +
294B HIS* 4.0 3.4 - - - +
295B PRO* 5.7 0.9 - - + -
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Residues in contact with GLN 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN* 4.7 1.0 - - - +
144A GLY* 5.9 0.9 - - - -
16B PRO* 3.6 1.9 - - - +
17B SER* 2.7 55.3 + - - +
18B PRO* 3.9 20.4 - - + +
77B SER* 3.1 32.1 + - - +
285B ILE* 2.8 26.3 + - - +
286B LEU* 3.4 29.1 - - - +
287B HIS 3.2 0.6 - - - -
288B ILE* 1.3 71.9 - - - +
290B VAL* 1.3 60.7 + - - +
293B LEU* 3.2 20.9 - - - +
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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
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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