Contacts of the strand formed by residues 671 - 676 (chain N) in PDB entry 2AS5
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 GLN 671 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580N VAL* 3.5 37.9 + - + +
583N GLN* 3.1 27.0 + - - +
657N ASN* 3.1 14.3 - - - +
658N PHE* 2.7 59.2 + - + +
659N TYR* 5.4 0.2 - - - -
668N SER* 5.1 0.3 + - - -
669N GLN* 3.4 12.0 + - - +
670N PRO* 1.3 78.5 + - - +
672N HIS* 1.3 65.3 + - - +
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Residues in contact with HIS 672 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583N GLN* 3.3 29.5 + - - +
586N ASP* 4.7 1.0 - - - +
655N LYS* 3.9 19.5 + - + +
656N VAL 4.0 1.3 - - - -
657N ASN* 3.5 15.9 + - - -
658N PHE* 3.5 2.3 - - - -
670N PRO* 5.1 7.6 + - + -
671N GLN* 1.3 80.4 - - - +
673N PHE* 1.3 64.6 + - - +
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Residues in contact with PHE 673 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585N THR 4.1 8.5 - - - -
586N ASP* 3.2 25.4 - - - -
587N SER* 3.0 30.3 - - - -
588N CYS* 3.9 0.7 - - - -
596N MET* 4.1 12.8 - - - -
611N PHE* 3.7 19.3 - + - -
642N ILE* 3.3 34.5 - - + -
655N LYS* 3.2 8.4 + - - +
656N VAL* 2.8 43.8 + - + +
658N PHE* 3.9 15.5 - + + -
672N HIS* 1.3 77.3 - - - +
674N THR* 1.3 82.6 + - - +
675N TYR* 3.9 28.0 - + - -
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Residues in contact with THR 674 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586N ASP* 3.0 10.8 + - - -
587N SER* 2.9 48.0 - - - -
588N CYS 3.3 2.3 + - - -
653N PRO* 5.6 1.6 - - + -
654N VAL 3.0 21.3 - - - +
655N LYS* 3.1 38.8 - - + +
656N VAL 4.6 0.9 - - - +
673N PHE* 1.3 79.1 - - - +
675N TYR* 1.3 59.1 + - - +
676N HIS* 4.3 13.4 + - - -
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Residues in contact with TYR 675 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588N CYS* 3.3 6.1 - - - -
589N LEU 3.8 16.8 - - - -
590N VAL* 4.1 17.6 - - + +
592N GLY* 5.1 0.4 - - - -
611N PHE* 4.0 3.1 - - - -
622N TRP* 3.6 26.1 - + - -
642N ILE* 3.4 19.3 - - + +
643N PRO* 2.6 47.5 + - - +
644N GLU* 5.0 0.4 - - - -
645N TYR* 3.8 24.5 - + + -
650N ILE* 5.5 0.5 - - - +
652N THR 4.7 0.3 - - - +
653N PRO* 3.4 4.2 - - - +
654N VAL* 3.1 39.0 + - + +
656N VAL* 3.7 28.3 - - + -
673N PHE* 3.9 12.3 - + - -
674N THR* 1.3 73.6 - - - +
676N HIS* 1.3 61.9 + - - +
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Residues in contact with HIS 676 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587N SER* 4.1 19.1 + - - -
588N CYS* 2.6 22.4 + - - +
589N LEU* 3.1 9.9 - - + +
590N VAL* 2.8 32.7 + - - +
650N ILE* 5.0 0.2 - - - -
653N PRO* 3.6 24.6 - - + +
674N THR* 4.3 16.5 + - - -
675N TYR* 1.3 76.4 - - - +
677N PRO* 1.3 72.8 - - + +
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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