Contacts of the strand formed by residues 479 - 485 (chain A) in PDB entry 3AR2
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 MET 479 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415A THR* 5.0 2.5 - - + -
419A LEU* 3.8 33.1 - - + +
475A ILE 3.6 2.2 + - - +
476A ARG* 2.6 24.2 + - - +
477A GLN 3.6 0.6 - - - -
478A LEU* 1.3 101.0 - - + +
480A LYS* 1.3 61.1 + - - +
481A LYS* 3.6 2.4 + - - +
498A CYS* 3.5 41.3 - - + +
499A SER* 3.5 11.4 - - - +
500A PRO* 3.9 11.0 - - + -
501A ALA* 4.4 4.0 - - - +
505A ARG 4.6 4.9 - - - +
506A ALA* 5.6 3.8 - - - +
509A GLY 5.3 1.3 - - - +
511A LYS* 4.2 12.1 - - + +
513A PHE* 3.7 20.9 - - + -
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Residues in contact with LYS 480 (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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479A MET* 1.3 72.5 - - - +
481A LYS* 1.3 66.2 + - - +
482A GLU* 3.2 25.3 + - - +
498A CYS* 3.0 23.7 - - - -
499A SER* 2.7 27.3 + - - +
500A PRO 4.4 7.7 - - - +
501A ALA* 4.7 7.6 - - + +
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Residues in contact with LYS 481 (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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418A ALA 5.8 0.2 + - - -
419A LEU* 3.3 32.0 + - + +
421A ASN 4.1 9.1 + - - -
422A ASP* 4.1 17.8 + - - +
476A ARG* 6.4 2.2 - - - +
479A MET 3.6 4.0 + - - -
480A LYS* 1.3 74.9 - - - +
482A GLU* 1.3 68.9 + - - +
483A PHE* 4.1 4.7 - - - +
484A THR* 3.7 18.9 - - + +
496A VAL* 3.4 25.1 - - + +
497A TYR 3.5 7.9 - - - +
498A CYS* 3.7 10.9 - - - -
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Residues in contact with GLU 482 (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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480A LYS* 3.2 27.4 + - - +
481A LYS* 1.3 75.1 - - - +
483A PHE* 1.3 68.3 + - + +
497A TYR* 2.6 39.1 + - + +
498A CYS* 4.3 1.1 - - - -
499A SER* 2.9 29.7 + - - +
510A ASN* 5.1 1.4 + - - +
573A ARG* 3.6 35.3 + - - +
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Residues in contact with PHE 483 (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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169A LYS 5.5 0.9 - - - +
171A THR* 5.5 1.3 - - + -
481A LYS* 4.1 3.5 - - - +
482A GLU* 1.3 81.0 - - + +
484A THR* 1.3 72.0 + - - +
485A LEU* 3.7 21.3 - - + -
496A VAL* 3.9 0.9 - - - -
497A TYR* 3.0 59.1 + + + +
512A MET* 5.5 0.9 - - + -
573A ARG* 3.4 40.2 - - + +
576A MET* 3.5 28.7 - - + -
578A LEU* 3.6 43.1 - - + -
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Residues in contact with THR 484 (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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169A LYS* 3.6 31.1 + - + +
170A SER* 4.8 1.4 - - - -
171A THR* 3.5 12.8 + - - +
422A ASP* 4.4 16.1 + - - +
481A LYS* 3.7 26.5 - - + +
483A PHE* 1.3 83.5 - - - +
485A LEU* 1.3 60.3 + - - +
486A GLU* 3.1 28.9 + - - +
494A MET* 4.9 3.4 - - - +
495A SER 3.9 4.9 + - - -
496A VAL* 3.9 13.7 - - - -
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Residues in contact with LEU 485 (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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171A THR* 4.5 0.9 - - + -
483A PHE* 3.7 17.4 + - + -
484A THR* 1.3 68.3 - - - +
486A GLU* 1.3 68.9 + - - +
491A ARG* 3.6 5.8 + - - +
494A MET* 3.8 0.3 - - - -
495A SER* 3.1 51.4 + - - +
496A VAL* 4.8 0.4 - - - +
497A TYR 6.2 0.4 - - - +
512A MET* 3.7 16.6 - - + -
576A MET* 5.5 0.2 - - - -
578A LEU* 3.7 29.6 - - + -
584A PHE* 3.8 45.1 - - + +
587A TYR* 3.9 24.2 - - + -
588A GLU* 4.3 1.1 - - - +
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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