Contacts of the helix formed by residues 20 - 28 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D TYR* 3.6 37.1 - - + +
12D ASP* 4.0 31.4 + - + +
15D GLU* 2.9 17.3 + - - +
18D PHE 3.9 0.2 + - - -
19D ASP* 1.3 69.9 - - - +
21D GLN* 1.3 65.6 + - - +
23D MET* 3.3 4.2 + - - +
24D GLU* 3.2 33.5 + - - +
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Residues in contact with GLN 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C GLN* 5.5 4.9 + - - -
19D ASP* 3.3 7.7 + - + +
20D LYS* 1.3 81.9 - - - +
22D THR* 1.3 64.7 - - - +
24D GLU* 3.5 6.7 + - - +
25D ILE* 3.2 34.7 + - + +
175D LEU* 3.9 29.5 - - + +
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Residues in contact with THR 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C TYR* 6.2 0.2 - - + -
18D PHE* 6.5 0.2 - - - -
19D ASP* 2.7 36.7 + - - +
20D LYS 3.3 0.2 - - - -
21D GLN* 1.3 76.1 - - - +
23D MET* 1.3 55.9 - - + +
25D ILE* 3.1 4.4 + - - +
26D HIS* 2.7 44.9 + - + +
171D HIS 3.7 21.7 + - - +
172D ALA* 3.8 21.3 - - - +
173D TYR 5.6 1.0 - - - -
175D LEU* 3.5 26.9 + - + +
176D LYS 4.8 0.5 + - - -
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Residues in contact with MET 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D LEU* 4.4 6.5 - - + -
9D TYR* 3.7 32.3 - - + +
11D TYR* 3.6 29.5 - - + +
14D LEU* 3.8 22.7 - - + -
18D PHE* 4.3 21.5 - - + +
19D ASP 3.2 16.5 + - - +
20D LYS 3.3 7.6 + - - +
22D THR* 1.3 77.9 - - - +
24D GLU* 1.3 56.9 + - - +
26D HIS* 4.0 5.6 - - - +
27D HIS* 3.1 31.5 + - - +
84D PHE* 6.0 0.9 - - - -
85D TRP* 4.0 30.1 - - + -
88D LEU* 4.5 1.8 - - + -
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Residues in contact with GLU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D TYR* 3.6 33.9 - - + -
20D LYS* 3.2 28.9 + - - +
21D GLN* 3.8 7.4 - - - +
22D THR 3.3 0.2 - - - -
23D MET* 1.3 78.9 - - - +
25D ILE* 1.3 52.5 - - + +
28D THR* 2.7 52.0 + - + +
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Residues in contact with ILE 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C TYR* 3.5 22.9 - - + +
178C GLN* 3.7 26.7 - - + +
179C ASN* 4.3 9.0 - - - +
21D GLN* 3.2 28.6 + - + +
22D THR* 3.1 4.6 + - - +
24D GLU* 1.3 75.5 - - + +
26D HIS* 1.3 61.4 + - - +
28D THR* 4.2 0.4 - - - -
29D LYS* 2.8 55.1 + - + +
30D HIS* 3.2 6.9 + - + -
175D LEU* 4.0 16.2 - - + -
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Residues in contact with HIS 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D THR* 2.7 31.3 + - + +
23D MET* 4.0 5.3 - - - +
25D ILE* 1.3 72.1 - - - +
27D HIS* 1.3 57.4 + - - +
30D HIS* 3.4 17.2 - - + +
31D HIS* 3.0 28.1 + - - +
81D HIS* 3.1 15.6 + + - -
84D PHE* 4.0 16.2 - + - -
85D TRP* 3.5 21.1 - + + -
167D ASP* 3.1 10.1 - - - -
171D HIS* 3.1 19.9 + + - +
172D ALA* 4.0 13.9 - - + -
206D MN 2.1 36.9 + - - -
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Residues in contact with HIS 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 3.7 25.5 - - + +
5D PRO 2.7 28.5 + - - -
6D SER* 4.4 2.9 - - - -
7D LEU* 3.4 33.3 - - + +
11D TYR* 2.8 30.5 + + + -
23D MET 3.1 19.6 + - - +
24D GLU 3.9 1.8 - - - +
26D HIS* 1.3 77.4 - - - +
28D THR* 1.3 66.3 + - + +
29D LYS 3.4 0.7 + - - -
31D HIS* 3.3 20.1 - - - +
32D GLN 3.4 5.4 + - - -
85D TRP* 3.7 25.5 - - + -
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Residues in contact with THR 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 4.7 6.5 - - + -
11D TYR* 3.4 25.8 - - + +
24D GLU* 2.7 34.6 + - + +
25D ILE* 4.2 0.2 - - - -
27D HIS* 1.3 78.1 - - + +
29D LYS* 1.3 78.9 + - - +
32D GLN* 3.2 21.1 - - - +
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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
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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