Contacts of the strand formed by residues 671 - 677 (chain A) in PDB entry 2YA6
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 LYS 671 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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644A LYS* 6.4 0.4 - - - +
654A LEU 3.4 1.2 - - - +
655A GLN* 3.3 3.1 - - - -
656A VAL* 2.8 48.0 + - + +
658A THR* 6.2 0.2 - - - +
669A ASP* 3.8 2.8 + - - +
670A ILE* 1.3 71.4 - - - +
672A ARG* 1.3 72.4 + - - +
673A TYR* 3.5 41.3 - - + +
721A GLU* 4.6 15.8 + - - -
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Residues in contact with ARG 672 (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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651A THR* 3.7 28.9 + - - +
653A ASP* 2.8 40.7 + - - +
654A LEU 3.1 6.1 - - - +
655A GLN* 4.3 13.7 - - + +
670A ILE* 3.7 8.9 + - + +
671A LYS* 1.3 89.6 - - - +
673A TYR* 1.3 68.2 + - - +
674A PRO* 3.6 10.9 - - + +
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Residues in contact with TYR 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A LYS* 5.3 3.8 + - - -
653A ASP* 4.0 3.4 - - - -
654A LEU* 2.8 23.9 + - + +
656A VAL* 3.5 35.5 - - + +
671A LYS* 3.5 35.7 - - + +
672A ARG* 1.3 77.2 - - - +
674A PRO* 1.4 58.9 - - + +
675A GLN* 3.1 18.8 - - - +
676A VAL* 3.1 27.6 + - - +
721A GLU* 4.5 6.2 + - - +
722A LEU* 3.5 56.1 + - + +
724A TRP* 3.3 31.0 - + + +
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Residues in contact with PRO 674 (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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653A ASP* 3.6 22.4 - - + +
672A ARG* 3.6 11.7 - - + +
673A TYR* 1.4 82.4 - - + +
675A GLN* 1.3 72.7 + - + +
676A VAL* 3.2 2.3 + - - -
677A LYS* 3.1 30.7 + - - +
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Residues in contact with GLN 675 (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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673A TYR* 3.3 27.1 - - - +
674A PRO* 1.3 88.5 - - + +
676A VAL* 1.3 57.5 + - - +
677A LYS* 4.1 1.7 + - - +
712A HIS* 4.9 1.0 + - - -
722A LEU 5.9 0.6 + - - -
723A THR* 6.1 0.8 - - - +
724A TRP* 3.9 41.4 + - + +
727A HIS* 3.1 25.4 + - + +
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Residues in contact with VAL 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A ASP* 3.4 2.6 - - - +
654A LEU* 2.9 45.6 + - + -
673A TYR 3.1 5.8 + - - +
674A PRO 4.3 2.7 - - - -
675A GLN* 1.3 81.3 - - - +
677A LYS* 1.3 68.9 + - - +
698A LEU* 4.4 7.9 - - + -
700A ASN* 4.1 6.7 - - - +
712A HIS* 3.5 34.5 - - + +
724A TRP* 3.7 46.9 - - + +
727A HIS* 4.1 6.3 - - + -
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Residues in contact with LYS 677 (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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652A GLY 3.5 13.2 - - - +
653A ASP* 4.9 3.8 - - + +
674A PRO* 3.1 29.2 + - - +
675A GLN 4.1 1.5 + - - +
676A VAL* 1.3 78.5 - - - +
678A ASP* 1.3 61.3 + - - +
679A VAL* 4.1 6.7 - - + -
700A ASN* 3.0 23.4 + - - +
701A ALA 4.1 4.8 - - - +
702A GLY* 4.1 23.6 - - - +
712A HIS* 5.0 3.5 + - - -
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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