Contacts of the strand formed by residues 501 - 506 (chain A) in PDB entry 3Q8A
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 VAL 501 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A ARG* 5.3 0.7 - - - +
369A THR* 4.1 16.4 - - + +
492A ILE* 3.4 3.9 - - - +
493A PHE 3.0 35.1 + - - +
496A LYS* 5.3 18.8 - - + -
499A ASN* 3.4 19.3 - - + +
500A LEU* 1.3 79.0 - - - +
502A GLU* 1.3 62.6 + - - +
503A ARG* 3.4 34.8 - - - +
531A PHE* 3.4 17.2 - - + -
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Residues in contact with GLU 502 (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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259A TYR* 2.8 28.6 + - - +
261A ILE* 3.4 24.6 - - + +
297A ARG* 4.4 21.7 + - - +
326A ASN* 5.3 2.9 - - - +
369A THR* 4.4 4.7 + - - +
485A GLN* 5.3 3.3 + - - -
490A ARG* 3.0 47.6 + - - -
491A ILE 3.3 5.8 - - - -
492A ILE* 4.2 9.2 - - + +
500A LEU 4.2 1.0 + - - -
501A VAL* 1.3 74.7 - - - +
503A ARG* 1.3 102.1 + - - +
504A ARG* 4.0 5.4 + - - -
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Residues in contact with ARG 503 (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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248A SER* 4.9 0.6 + - - -
250A GLU* 2.7 34.4 + - - +
256A VAL* 5.4 5.4 - - + -
257A ALA 5.8 1.1 - - - -
259A TYR* 3.7 6.1 - - - -
261A ILE* 5.4 0.4 - - - -
369A THR 3.2 23.2 + - - -
370A GLY* 3.6 17.8 + - - -
371A THR* 3.5 21.2 - - - +
408A ASN* 6.0 3.6 - - - +
490A ARG* 3.4 2.4 - - - +
491A ILE 2.9 22.6 + - - +
501A VAL* 3.4 15.0 - - - +
502A GLU* 1.3 95.9 + - - +
504A ARG* 1.3 75.8 + - - +
505A ILE* 4.5 2.0 - - + -
530A ALA* 4.4 15.2 + - + +
531A PHE* 3.3 39.8 - - + -
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Residues in contact with ARG 504 (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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256A VAL* 3.8 5.2 - - - +
257A ALA* 3.1 35.9 + - + -
259A TYR* 3.1 32.4 + - - +
326A ASN* 3.4 23.2 + - - +
484A ILE* 4.3 9.0 - - - -
485A GLN* 3.8 30.5 + - - +
488A THR* 3.1 48.0 + - - +
489A ALA 3.5 5.6 - - - +
490A ARG* 3.4 36.7 - - + +
502A GLU* 4.0 6.5 + - - -
503A ARG* 1.3 88.7 - - - +
505A ILE* 1.3 65.9 + - - +
586A LYS* 5.7 1.4 - - - +
587A MET 4.8 0.8 + - - -
588A ASN* 4.2 5.5 + - - -
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Residues in contact with ILE 505 (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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255A LEU 3.2 7.4 - - - +
256A VAL* 5.2 0.9 - - + -
488A THR* 3.8 3.6 - - - -
489A ALA* 2.9 33.0 + - - +
491A ILE* 3.4 33.0 - - + -
503A ARG* 4.5 1.8 - - + -
504A ARG* 1.3 90.3 - - - +
506A ALA* 1.3 67.4 + - - +
507A ALA* 3.3 3.1 + - - +
521A MET* 3.4 45.3 - - + -
526A ALA* 4.0 8.7 - - + -
529A ILE* 3.6 11.7 - - + -
530A ALA* 3.7 28.9 - - + -
583A LEU* 4.7 3.1 - - + -
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Residues in contact with ALA 506 (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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228A THR* 3.9 36.8 - - + +
229A ALA* 4.2 2.9 - - - +
255A LEU* 2.8 29.7 + - + +
487A THR 4.2 4.9 - - - -
488A THR* 4.3 4.9 - - - +
505A ILE* 1.3 73.6 - - - +
507A ALA* 1.3 56.7 + - - +
518A LYS* 3.8 12.8 - - + +
519A PRO 4.8 3.9 - - - +
521A MET* 3.4 22.2 - - - +
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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