Contacts of the strand formed by residues 697 - 700 (chain A) in PDB entry 3NKO
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 697 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623A MET* 4.1 2.9 - - - +
624A PRO* 4.7 1.2 - - - +
648A VAL* 3.8 22.7 - - + -
660A GLN* 2.9 44.5 + - - +
661A ASN 5.6 0.2 - - - -
662A CYS* 4.6 6.3 - - - -
665A TYR* 4.0 13.9 - - + -
673A TYR* 3.3 45.3 - - + -
674A GLY 3.3 6.5 - - - +
675A PHE* 3.8 14.8 - - + -
693A LEU 3.8 3.1 + - - +
694A VAL* 3.5 32.8 - - - +
695A THR 3.5 1.2 - - - -
696A ASN* 1.3 77.8 - - - +
698A VAL* 1.3 70.4 + - - +
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Residues in contact with VAL 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A MET* 4.1 24.2 - - + -
624A PRO* 4.6 1.1 - - + -
660A GLN* 4.4 0.9 - - - +
665A TYR* 3.9 4.7 - - - -
673A TYR* 3.2 3.2 - - - -
674A GLY 2.8 37.0 + - - +
675A PHE 4.6 0.2 - - - +
676A LEU* 4.0 34.3 - - + -
696A ASN 4.8 0.2 - - - +
697A MET* 1.3 81.6 - - - +
699A PRO* 1.3 66.9 - - + +
700A MET* 3.6 29.4 - - + -
732A PRO* 5.4 0.9 - - + -
763A TYR* 3.4 19.7 - - + +
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Residues in contact with PRO 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A MET* 3.8 16.6 - - + -
660A GLN* 4.7 0.7 - - - +
665A TYR* 3.4 22.8 - - + +
671A MET* 3.9 12.8 - - + -
672A SER 3.6 4.0 - - - +
698A VAL* 1.3 86.7 - - + +
700A MET* 1.3 59.5 + - - +
752A VAL* 3.8 16.8 - - + -
757A ILE* 4.0 8.5 - - + -
758A PRO 3.6 21.3 - - - +
759A VAL* 4.4 3.4 - - + -
760A PRO* 3.9 5.2 - - + -
763A TYR* 2.6 28.1 + - - +
793A HIS* 3.2 11.6 - - - -
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Residues in contact with MET 700 (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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671A MET* 3.5 4.9 - - - -
672A SER* 2.9 36.7 + - - -
674A GLY* 3.9 16.4 - - - +
698A VAL* 3.4 30.4 + - + +
699A PRO* 1.3 80.0 - - - +
701A TYR* 1.3 65.1 + - - +
704A PHE* 3.7 20.2 - - + -
705A LYS* 3.7 19.6 - - + +
708A TRP* 3.3 55.9 - - + +
763A TYR* 4.0 18.4 - - + +
793A HIS* 3.4 3.8 - - - -
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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