Contacts of the strand formed by residues 432 - 440 (chain A) in PDB entry 2YWH
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 ILE 432 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407A PHE* 5.4 4.7 - - + -
430A ARG 4.6 4.9 - - - +
431A GLY* 1.3 75.0 - - - +
433A GLN* 1.3 74.6 + - - +
434A LYS* 3.4 19.4 + - - +
448A TYR* 3.3 2.9 - - - -
449A GLU* 2.9 40.7 + - + +
481A ARG* 4.2 22.7 - - - +
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Residues in contact with GLN 433 (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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423A ILE* 4.0 11.8 - - - +
431A GLY 4.0 0.2 + - - -
432A ILE* 1.3 81.9 - - - +
434A LYS* 1.3 65.1 + - - +
435A ASN* 3.8 18.1 - - - +
436A MET* 3.7 28.6 - - - +
446A LEU* 4.0 8.3 - - - +
447A GLU 3.6 2.7 - - - +
448A TYR* 2.9 49.0 + - + +
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Residues in contact with LYS 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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409A LEU* 5.1 2.9 - - + -
432A ILE* 4.0 11.3 - - + +
433A GLN* 1.3 80.4 - - - +
435A ASN* 1.3 65.3 + - - +
447A GLU* 2.9 24.3 + - + +
449A GLU* 3.5 50.0 - - + +
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Residues in contact with ASN 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 GLN* 3.7 10.4 - - - +
434A LYS* 1.3 84.5 - - - +
436A MET* 1.3 71.9 + - - +
437A THR* 3.5 28.3 - - - +
445A TYR* 3.5 22.6 - - - -
446A LEU* 3.6 2.1 - - - -
447A GLU* 3.1 44.8 + - + +
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Residues in contact with MET 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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419A VAL* 4.5 11.0 - - + -
423A ILE* 4.6 9.6 - - + -
433A GLN* 3.7 19.7 - - - +
435A ASN* 1.3 82.1 + - - +
437A THR* 1.3 70.4 + - - +
438A TYR* 3.5 34.1 - - + +
444A VAL* 4.0 13.0 - - + -
445A TYR 3.2 6.1 - - - +
446A LEU* 3.3 24.9 - - + -
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Residues in contact with THR 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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435A ASN* 3.5 24.7 - - - +
436A MET* 1.3 82.1 - - - +
438A TYR* 1.3 68.9 + - - +
439A LEU* 4.3 6.4 - - - +
444A VAL* 3.3 4.2 - - - +
445A TYR* 2.5 62.6 + - + +
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Residues in contact with TYR 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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416A LYS* 4.8 10.1 - - + -
436A MET* 3.5 29.3 - - + +
437A THR* 1.3 81.4 + - - +
439A LEU* 1.3 62.4 + - - +
440A ASP* 3.1 20.3 + - - +
441A PRO* 4.7 10.3 - - + -
443A THR 3.1 8.7 - - - -
444A VAL* 3.4 26.7 - - + -
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Residues in contact with LEU 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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110A ILE* 4.8 12.3 - - + +
115A VAL* 5.5 0.7 - - + -
148A GLN* 4.4 15.8 - - - +
151A GLU* 4.3 11.1 - - - +
152A VAL* 3.6 45.8 - - + +
413A ILE* 3.6 36.6 - - + -
437A THR* 4.3 4.3 - - - +
438A TYR* 1.3 73.7 - - - +
440A ASP* 1.3 63.7 + - - +
443A THR* 2.6 34.7 + - + +
445A TYR* 3.8 27.6 - - + -
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Residues in contact with ASP 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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144A ARG* 3.3 18.0 + - + -
147A LYS* 6.4 2.7 - - + -
148A GLN* 3.2 24.8 + - + +
151A GLU* 5.1 6.7 - - - +
438A TYR* 3.1 15.5 - - - +
439A LEU* 1.3 75.1 - - - +
441A PRO* 1.3 78.0 - - + +
442A ASN* 2.6 36.2 + - - +
443A THR* 2.8 36.8 + - - +
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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