Contacts of the strand formed by residues 423 - 431 (chain B) in PDB entry 4WGK
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 LEU 423 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B TYR* 3.5 27.1 - - + -
144B MET* 3.6 34.5 - - + +
145B ALA* 3.6 15.3 - - - +
146B GLU* 2.9 18.2 + - - +
151B ASN* 3.5 43.2 - - - +
153B THR* 4.1 9.4 - - + +
422B PRO* 1.3 77.4 - - - +
424B ALA* 1.3 64.2 + - - +
528B THR 3.4 2.2 - - - +
529B LEU* 3.7 36.3 - - + -
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Residues in contact with ALA 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ASN* 5.6 0.7 - - - -
153B THR* 4.2 3.9 - - - +
422B PRO* 5.2 3.1 - - + +
423B LEU* 1.3 76.9 - - - +
425B SER* 1.3 64.9 - - - +
527B ILE* 3.6 4.5 - - - +
528B THR* 2.9 44.4 + - - +
617B ILE* 3.8 22.0 - - + +
622B VAL* 6.2 1.6 - - + -
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Residues in contact with SER 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B THR* 4.9 2.5 - - - -
184B ARG* 4.6 2.1 + - - -
186B ASP* 2.9 48.9 + - - +
187B ASN* 3.8 13.8 - - - +
424B ALA* 1.3 79.5 - - - +
426B ALA* 1.3 61.8 + - - +
526B ILE 3.3 8.7 - - - -
527B ILE* 4.1 4.7 - - - -
617B ILE* 4.4 4.6 - - - +
622B VAL* 3.5 18.2 - - - +
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Residues in contact with ALA 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ASP* 4.6 3.1 - - - +
425B SER* 1.3 75.5 - - - +
427B HIS* 1.3 60.3 + - - +
525B GLN* 3.1 6.2 - - - +
526B ILE 2.9 32.7 + - - +
613B LEU* 4.0 14.9 - - + +
617B ILE* 3.7 25.1 - - + +
622B VAL* 4.0 17.7 - - + -
625B LEU* 4.1 13.9 - - + -
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Residues in contact with HIS 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 3.7 9.0 + - - -
185B ARG* 3.5 41.6 + - - -
186B ASP* 3.5 27.3 - - + +
426B ALA* 1.3 75.8 - - - +
428B GLN* 1.3 94.2 + - - +
429B TRP* 3.6 17.5 - + - -
523B ASP* 2.5 35.5 + - + +
524B VAL 3.4 7.9 - - - -
525B GLN* 3.8 17.3 - - + -
613B LEU* 4.9 2.7 - - - +
622B VAL* 5.0 1.8 - - - +
625B LEU* 4.5 8.1 - - - +
627B ARG* 5.2 3.2 + - - +
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Residues in contact with GLN 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B HIS* 1.3 90.1 + - - +
429B TRP* 1.3 62.8 + - - +
430B VAL* 4.1 14.4 - - + +
522B VAL 3.5 1.7 - - - +
523B ASP* 3.6 3.1 - - - -
524B VAL* 2.9 45.0 + - + +
609B LEU* 4.7 8.0 - - - +
612B ASN* 4.8 6.4 + - - +
613B LEU* 4.1 13.4 - - + +
625B LEU* 3.9 22.4 - - + +
626B SER* 2.8 51.5 + - - +
627B ARG 4.1 2.9 - - - -
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Residues in contact with TRP 429 (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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165B GLN* 5.1 0.6 + - - -
168B ARG* 5.8 0.2 - - - +
169B LEU* 5.0 11.0 - - + +
172B LEU* 6.4 0.7 - - + -
185B ARG* 3.5 40.6 - - + -
427B HIS* 3.8 7.5 - + - -
428B GLN* 1.3 76.8 - - - +
430B VAL* 1.3 61.7 + - - +
521B ILE* 3.8 7.9 - - + -
522B VAL 3.6 0.7 - - - -
523B ASP* 2.8 36.1 + - - -
627B ARG* 3.2 61.6 + - + +
628B GLY* 3.4 23.3 - - - -
629B PRO* 3.1 27.4 - - - +
630B GLU* 3.9 15.0 - - + -
631B PRO* 3.3 33.2 - - + +
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Residues in contact with VAL 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B GLN* 4.1 13.5 - - - +
429B TRP* 1.3 81.6 - - - +
431B ASP* 1.3 63.4 + - - +
432B MET* 3.0 13.3 + - - +
435B VAL* 3.8 21.5 - - + -
520B ASP 3.2 0.3 - - - +
521B ILE* 3.5 4.4 - - - +
522B VAL* 2.9 40.7 + - - +
524B VAL* 3.7 29.6 - - + -
609B LEU* 3.7 32.5 - - + -
629B PRO* 4.8 0.7 - - - -
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Residues in contact with ASP 431 (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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430B VAL* 1.3 72.0 - - - +
432B MET* 1.3 57.0 + - - +
433B THR* 3.0 32.5 + - - +
434B ASP* 3.1 27.7 + - + +
435B VAL* 3.3 11.6 - - - +
520B ASP* 3.5 15.2 - - - +
521B ILE* 4.2 16.3 - - + +
629B PRO* 4.4 12.5 - - + +
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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