Contacts of the strand formed by residues 695 - 702 (chain A) in PDB entry 4NAM
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 695 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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645A GLU 3.8 0.2 - - - +
646A ILE* 3.3 7.5 - - - +
647A GLU* 2.8 62.5 + - + +
693A ASN 4.4 2.9 - - - +
694A TYR* 1.3 77.8 - - - +
696A VAL* 1.3 62.7 + - - +
697A ASN* 3.9 11.8 + - - +
728A SER* 4.0 16.3 + - - +
729A LYS 3.5 6.5 - - - +
730A LYS* 3.9 32.8 - - + +
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Residues in contact with VAL 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A VAL* 4.7 1.6 - - + -
645A GLU 3.5 6.7 - - - +
646A ILE* 4.8 4.9 - - + -
678A PHE* 4.2 21.3 - - + -
687A LEU* 4.1 28.0 - - + -
689A ILE* 3.7 32.1 - - + -
694A TYR 5.6 0.4 - - - +
695A LYS* 1.3 73.5 - - - +
697A ASN* 1.3 61.8 + - - +
698A VAL* 4.3 8.3 - - + -
727A PHE* 3.7 13.7 - - + -
728A SER* 3.2 4.9 - - - -
729A LYS 2.9 36.6 + - - +
731A GLY 5.7 0.2 - - - +
734A ILE* 4.8 8.1 - - + -
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Residues in contact with ASN 697 (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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643A ILE 3.8 0.7 - - - +
644A VAL* 3.6 2.8 - - - +
645A GLU* 2.8 61.7 + - - +
647A GLU* 3.0 31.2 + - - +
653A LYS* 4.4 0.3 + - - -
695A LYS* 3.9 10.5 - - - +
696A VAL* 1.3 76.6 - - - +
698A VAL* 1.3 62.3 - - - +
699A TYR* 3.6 16.7 + - + +
725A LEU* 4.1 6.6 - - + +
727A PHE 3.3 2.9 - - - -
728A SER* 2.7 32.7 + - - -
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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
----------------------------------------------------------
627A LEU* 4.0 5.8 - - + -
642A TYR* 4.2 20.9 - - + -
643A ILE 3.4 9.0 - - - +
644A VAL* 4.6 6.3 - - + -
676A ILE* 4.4 13.0 - - + -
678A PHE* 3.8 31.6 - - + -
696A VAL* 4.3 3.4 - - + -
697A ASN* 1.3 78.0 - - - +
699A TYR* 1.3 64.4 + - - +
725A LEU* 3.6 2.9 - - - +
726A ILE* 2.9 37.7 + - + +
727A PHE* 2.9 37.6 + - + +
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Residues in contact with TYR 699 (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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642A TYR* 3.1 11.9 - - - -
643A ILE* 2.9 46.2 + - + +
645A GLU* 2.5 41.5 + - + -
653A LYS* 3.6 12.5 + - - -
697A ASN* 3.6 22.4 + - + +
698A VAL* 1.3 75.3 - - - +
700A ALA* 1.3 60.1 + - - +
701A VAL* 4.6 0.2 - - - +
723A LYS* 3.5 56.3 + - + -
724A ILE 3.1 6.7 - - - +
725A LEU* 3.5 37.3 - - + +
726A ILE* 4.2 0.4 - - - -
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Residues in contact with ALA 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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612A VAL* 4.1 19.3 - - + -
616A HIS* 4.5 0.4 - - + -
639A LEU* 4.0 19.5 - - + -
641A GLY 3.8 0.4 - - - -
642A TYR* 3.7 25.4 - - + -
699A TYR* 1.3 74.3 - - - +
701A VAL* 1.3 61.7 + - - +
702A THR 4.1 0.4 - - - -
723A LYS* 3.5 3.3 - - - -
724A ILE* 2.8 42.5 + - + +
726A ILE* 4.0 6.9 - - + +
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Residues in contact with VAL 701 (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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639A LEU* 3.5 6.9 - - - -
640A SER* 2.9 38.1 + - - +
641A GLY 2.9 15.7 + - - +
643A ILE* 3.9 30.1 - - + -
663A LEU* 4.0 15.0 - - + -
699A TYR 4.6 1.1 - - - +
700A ALA* 1.3 75.6 - - - +
702A THR* 1.3 72.0 + - - +
705A ASN 4.0 7.6 - - - +
706A THR* 3.8 6.3 - - - +
721A ILE* 3.9 19.7 - - + -
722A LYS 4.2 5.8 - - - +
723A LYS* 4.1 9.4 - - + -
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Residues in contact with THR 702 (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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605A VAL 3.7 7.9 - - - -
606A GLY* 3.9 13.9 - - - -
607A ALA 4.4 6.7 - - - +
612A VAL* 4.6 2.0 - - + -
638A ILE* 3.3 14.1 - - + +
639A LEU* 3.9 15.9 - - + -
700A ALA 4.2 0.4 + - - -
701A VAL* 1.3 74.6 - - - +
703A LYS* 1.3 63.3 + - - +
704A GLU* 3.6 9.4 + - - +
705A ASN* 2.9 39.1 + - - +
706A THR* 2.7 17.1 + - - -
722A LYS 5.0 0.4 + - - -
724A ILE* 4.0 24.9 - - + +
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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