Contacts of the helix formed by residues 433 - 441 (chain A) in PDB entry 2WP9
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 SER 433 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 5.3 2.0 - - - -
431A ASP 3.6 1.6 + - - -
432A ALA* 1.3 76.7 - - - +
434A GLU* 1.3 65.2 + - - +
435A SER* 3.4 9.8 + - - -
436A ASP* 2.7 39.6 + - - -
437A VAL* 3.2 13.8 + - - +
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Residues in contact with GLU 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 2.8 51.9 + - + +
2A LYS* 3.3 36.8 + - - +
433A SER* 1.3 74.2 - - - +
435A SER* 1.3 58.0 + - - +
437A VAL* 3.4 4.6 + - - +
438A GLU* 3.0 28.3 + - + +
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Residues in contact with SER 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433A SER* 3.3 8.1 + - - -
434A GLU* 1.3 76.4 - - - +
436A ASP* 1.3 63.4 + - - +
437A VAL 3.2 0.2 - - - -
438A GLU* 3.6 10.2 - - - +
439A ALA* 2.9 29.8 + - - +
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Residues in contact with ASP 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A VAL* 4.0 10.4 - - + +
171A LYS 3.2 26.2 + - - +
172A ASN* 3.9 11.2 - - - -
173A GLN* 4.0 8.9 + - - +
431A ASP 4.4 1.0 - - - +
432A ALA* 3.6 12.0 - - + -
433A SER* 2.7 40.5 + - - +
435A SER* 1.3 79.3 + - - +
437A VAL* 1.3 62.7 + - - +
439A ALA* 3.5 14.9 + - - +
440A SER* 3.7 5.2 + - - -
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Residues in contact with VAL 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.5 18.6 - - + -
3A LEU* 3.7 30.1 - - + -
170A VAL* 4.2 13.9 - - + -
181A THR* 4.1 10.5 - - + -
192A TYR* 3.7 35.7 - - + -
432A ALA* 4.3 3.1 - - + -
433A SER 3.2 10.6 + - - +
434A GLU 3.7 8.1 - - - +
435A SER 3.2 0.6 - - - -
436A ASP* 1.3 76.7 - - - +
438A GLU* 1.3 70.5 - - - +
440A SER* 3.0 23.2 + - - -
441A LEU* 3.7 4.7 + - + +
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Residues in contact with GLU 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 6.0 0.2 - - - +
434A GLU* 3.0 20.0 + - + +
435A SER* 3.6 12.6 - - - +
437A VAL* 1.3 80.2 - - - +
439A ALA* 1.3 61.3 + - - +
441A LEU* 2.9 34.8 + - - +
442A ASP* 3.7 10.0 + - - +
445A ASN* 3.7 22.0 + - - -
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Residues in contact with ALA 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A SER 2.9 16.5 + - - +
436A ASP* 3.6 9.2 - - - +
437A VAL 3.1 0.4 + - - -
438A GLU* 1.3 75.9 - - - +
440A SER* 1.3 62.0 + - - +
441A LEU 3.0 1.0 + - - -
442A ASP* 3.2 31.1 + - - +
443A ARG 4.9 0.2 + - - -
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Residues in contact with SER 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A LEU* 4.5 4.7 - - - +
168A ASP* 3.6 29.1 - - - +
169A LEU 3.0 23.9 + - - -
170A VAL* 3.1 16.8 - - - +
181A THR* 3.3 28.6 + - - -
436A ASP 3.7 2.7 + - - -
437A VAL 3.0 14.7 + - - -
439A ALA* 1.3 76.4 - - - +
441A LEU* 1.3 59.7 + - - +
442A ASP 3.4 0.4 - - - -
443A ARG* 4.7 2.1 + - - +
444A LEU 5.1 1.0 + - - -
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Residues in contact with LEU 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 4.0 28.9 - - + -
167A LEU* 3.9 10.8 - - + -
181A THR* 3.9 21.8 - - + +
190A VAL* 3.8 24.9 - - + -
437A VAL* 4.0 10.3 - - + +
438A GLU* 2.9 31.3 + - - +
440A SER* 1.3 77.5 - - - +
442A ASP* 1.3 59.6 + - - +
443A ARG 3.3 2.5 - - - -
444A LEU* 3.1 14.4 + - + +
445A ASN* 2.9 42.6 + - - +
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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