Contacts of the strand formed by residues 671 - 676 (chain M) in PDB entry 2O93
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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669L GLN* 2.5 39.9 + - - +
580M VAL* 3.2 46.8 + - + +
581M GLU 5.5 1.6 - - - -
583M GLN* 4.0 13.0 - - - +
657M ASN* 3.1 16.9 + - - -
658M PHE* 2.8 64.8 + - + +
659M TYR* 5.1 0.9 - - - -
669M GLN 3.3 9.6 - - - +
670M PRO* 1.3 83.9 - - - +
672M HIS* 1.3 65.0 + - - +
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Residues in contact with HIS 672 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580L VAL 4.2 9.7 + - - -
581L GLU 3.9 19.4 + - - -
582L ARG* 5.0 1.8 - - - -
583L GLN* 5.7 1.6 - - - -
669L GLN* 6.1 2.2 - - - -
671L GLN* 2.8 37.7 + - - -
672L HIS* 5.7 8.7 - + - -
583M GLN* 3.2 29.3 + - - +
586M ASP* 4.7 3.9 - - - +
655M LYS* 5.4 14.2 - - + +
656M VAL 3.9 3.1 + - - +
657M ASN* 3.4 14.5 + - - -
658M PHE* 3.9 1.3 - - - -
670M PRO 4.6 5.6 + - - -
671M GLN* 1.3 79.9 - - - +
673M PHE* 1.3 63.9 + - - +
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Residues in contact with PHE 673 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583M GLN* 4.5 0.4 - - - -
585M THR* 3.6 24.7 - - + -
586M ASP* 3.6 14.1 - - - -
587M SER 3.5 25.6 - - - -
588M CYS* 3.8 3.4 - - - -
596M MET* 4.1 12.3 - - - -
611M PHE* 3.8 14.4 - + + -
642M ILE* 3.2 45.5 - - + -
655M LYS* 3.7 5.7 - - - +
656M VAL* 3.0 42.2 + - + +
658M PHE* 4.1 14.8 - + + -
672M HIS* 1.3 76.4 - - - +
674M THR* 1.3 90.2 + - - +
675M TYR* 3.8 10.3 - + - -
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Residues in contact with THR 674 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586M ASP 3.0 14.0 + - - -
587M SER* 3.1 29.8 - - - -
588M CYS 3.4 4.0 + - - -
653M PRO* 4.1 13.7 - - + -
654M VAL 3.0 29.2 - - - +
655M LYS* 4.2 15.4 - - + +
656M VAL 4.5 0.7 - - - +
673M PHE* 1.3 86.8 + - - +
675M TYR* 1.3 70.2 + - - +
676M HIS* 4.2 10.1 - - + -
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Residues in contact with TYR 675 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588M CYS* 3.5 15.7 - - - -
589M LEU 3.8 9.0 - - - -
590M VAL* 4.1 17.3 - - + -
611M PHE* 3.8 4.9 - + - -
622M TRP* 3.7 11.0 - + - -
642M ILE* 3.6 18.6 - - + +
643M PRO* 2.8 44.9 + - - +
645M TYR* 3.2 44.4 - + + -
650M ILE* 3.8 2.5 - - - +
653M PRO* 3.3 4.3 - - - +
654M VAL* 2.7 42.7 + - + +
656M VAL* 3.7 21.8 - - + -
673M PHE* 3.8 9.6 - + - -
674M THR* 1.3 74.8 - - - +
676M HIS* 1.3 63.0 + - - +
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Residues in contact with HIS 676 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587M SER* 3.4 38.2 + - - -
588M CYS* 3.1 16.9 + - - +
589M LEU* 3.7 7.5 - - + -
590M VAL* 3.5 23.4 + - - +
650M ILE* 4.2 2.5 - - - -
653M PRO* 3.6 31.2 - - + +
674M THR* 4.2 9.8 - - + -
675M TYR* 1.3 73.5 - - - +
677M PRO* 1.3 75.2 - - + +
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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