Contacts of the helix formed by residues 20 - 28 (chain B) in PDB entry 1VEW
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 20 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B TYR* 3.5 37.7 - - + +
12B ASP* 4.0 29.4 + - + +
15B GLU* 2.9 19.2 + - - +
18B PHE 3.8 0.2 + - - -
19B ASP* 1.3 69.2 - - - +
21B GLN* 1.3 66.2 + - - +
23B MET* 3.3 4.0 + - - +
24B GLU* 3.2 34.6 + - - +
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Residues in contact with GLN 21 (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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178A GLN* 5.4 5.4 + - - -
19B ASP* 3.3 8.0 + - + +
20B LYS* 1.3 81.1 - - - +
22B THR* 1.3 63.3 - - - +
24B GLU* 3.5 6.7 + - - +
25B ILE* 3.2 34.8 + - + +
175B LEU* 3.8 29.5 - - + +
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Residues in contact with THR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A TYR* 6.2 0.2 - - + -
19B ASP* 2.7 36.1 + - - +
20B LYS 3.3 0.4 - - - -
21B GLN* 1.3 74.5 - - - +
23B MET* 1.3 58.9 + - + +
25B ILE* 3.2 4.4 + - - +
26B HIS* 2.8 45.7 + - + +
171B HIS 3.7 23.7 + - - +
172B ALA* 3.8 19.5 - - - +
173B TYR* 5.3 1.3 - - - -
175B LEU* 3.5 26.7 + - + +
176B LYS 4.8 0.2 + - - -
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Residues in contact with MET 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 4.4 6.7 - - + -
9B TYR* 3.7 31.6 - - + +
11B TYR* 3.5 35.1 - - + +
14B LEU* 3.8 22.9 - - + -
18B PHE* 4.4 21.3 - - + +
19B ASP 3.2 17.8 + - - +
20B LYS 3.3 3.5 + - - +
22B THR* 1.3 77.9 - - - +
24B GLU* 1.3 56.0 + - - +
26B HIS* 4.0 6.2 - - - +
27B HIS* 3.1 31.2 + - - +
84B PHE* 5.9 0.9 - - - -
85B TRP* 4.0 30.2 - - + -
88B LEU* 4.5 1.6 - - + -
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Residues in contact with GLU 24 (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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11B TYR* 3.6 34.2 - - + -
20B LYS* 3.2 28.9 + - - +
21B GLN* 3.7 7.1 - - - +
22B THR 3.3 0.2 - - - -
23B MET* 1.3 77.3 - - - +
25B ILE* 1.3 58.1 + - + +
28B THR* 2.7 48.5 + - + +
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Residues in contact with ILE 25 (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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174A TYR* 3.4 24.0 - - + +
178A GLN* 3.8 27.4 - - + -
179A ASN* 4.3 9.4 - - - +
21B GLN* 3.2 28.3 + - + +
22B THR* 3.8 4.0 - - + +
24B GLU* 1.3 74.0 - - + +
26B HIS* 1.3 60.6 + - - +
28B THR* 4.2 0.7 - - - -
29B LYS* 2.8 54.4 + - + +
30B HIS* 3.2 7.5 + - + +
175B LEU* 4.0 15.9 - - + -
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Residues in contact with HIS 26 (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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174A TYR* 5.3 0.2 + - - -
22B THR* 2.8 30.8 + - + +
23B MET* 4.0 6.0 - - - +
25B ILE* 1.3 71.3 - - - +
27B HIS* 1.3 58.0 + - - +
30B HIS* 3.3 16.8 - - + +
31B HIS* 3.0 26.3 + - - +
81B HIS* 3.1 15.8 + + - -
84B PHE* 4.1 13.7 - + - -
85B TRP* 3.5 21.1 - + + -
167B ASP* 3.1 9.6 - - - -
171B HIS* 3.1 15.8 + + - +
172B ALA* 3.9 20.1 - - + -
206B MN 2.1 36.9 + - - -
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Residues in contact with HIS 27 (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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4B LEU* 3.7 26.5 - - + +
5B PRO 2.7 28.1 + - - -
6B SER* 4.4 3.6 - - - -
7B LEU* 3.5 32.0 - - + +
11B TYR* 2.8 30.3 + - + -
23B MET 3.1 19.6 + - - +
24B GLU 3.9 1.1 - - - +
26B HIS* 1.3 76.7 - - - +
28B THR* 1.3 68.0 + - + +
29B LYS 3.5 0.2 + - - -
31B HIS* 3.3 19.5 - - - +
32B GLN 3.4 6.6 + - - -
85B TRP* 3.7 25.3 - - + -
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Residues in contact with THR 28 (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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4B LEU* 4.7 5.8 - - + -
11B TYR* 3.4 26.5 - - + +
24B GLU* 2.7 34.8 + - + +
25B ILE* 4.2 0.3 - - - -
27B HIS* 1.3 77.5 - - + +
29B LYS* 1.3 79.4 + - - +
32B GLN* 3.2 20.3 - - - +
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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