Contacts of the strand formed by residues 641 - 648 (chain A) in PDB entry 5NK4
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 VAL 641 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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631A MET* 3.3 6.6 - - - +
632A LEU* 2.8 58.1 + - + +
640A GLU* 1.3 85.5 - - - +
642A PRO* 1.3 75.2 - - + +
643A VAL* 4.3 4.7 - - + -
679A GLU* 5.5 5.6 - - - +
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Residues in contact with PRO 642 (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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629A LYS* 4.2 15.9 - - - +
630A GLY 3.3 10.3 - - - +
631A MET* 3.8 13.0 - - + -
640A GLU 4.4 1.8 - - - +
641A VAL* 1.3 92.2 - - + +
643A VAL* 1.3 67.1 + - - +
693A GLU* 4.8 1.6 - - - -
694A TYR* 3.8 27.2 + - + +
696A GLU* 6.2 0.4 - - - +
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Residues in contact with VAL 643 (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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613A VAL* 5.5 1.1 - - + -
629A LYS* 3.6 3.6 - - - -
630A GLY 2.9 45.8 + - - +
631A MET 3.9 13.0 - - - +
632A LEU* 3.6 27.1 - - + +
641A VAL* 4.1 5.8 - - + +
642A PRO* 1.3 80.5 - - - +
644A ALA* 1.3 59.8 + - - +
645A ILE* 3.9 18.8 - - + -
679A GLU* 4.2 8.1 - - + -
691A ILE* 3.7 18.2 - - + -
692A THR 3.3 15.7 - - - +
693A GLU* 5.1 0.7 - - - -
694A TYR* 3.6 11.5 - - - +
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Residues in contact with ALA 644 (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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619A ILE* 4.9 0.9 - - + -
627A VAL* 4.7 2.5 - - + -
628A TYR 3.2 8.1 - - - +
643A VAL* 1.3 74.7 - - - +
645A ILE* 1.3 61.5 + - - +
691A ILE* 3.3 5.9 - - - +
692A THR* 2.9 36.9 + - - +
693A GLU 4.0 0.7 - - - +
694A TYR* 3.9 6.5 - - + +
1001A 90E 3.3 53.4 - - + +
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Residues in contact with ILE 645 (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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613A VAL* 3.7 23.1 - - + -
614A THR 4.0 2.2 - - - +
615A ARG* 3.9 23.6 - - + -
627A VAL* 3.2 2.9 - - - -
628A TYR* 2.7 46.2 + - + +
629A LYS 4.5 0.2 - - - -
630A GLY* 3.7 31.6 - - - +
643A VAL* 3.9 13.2 - - + -
644A ALA* 1.3 80.2 - - - +
646A LYS* 1.3 61.2 + - - +
647A THR* 4.4 2.9 - - + -
689A MET* 3.6 38.1 - - + -
690A ILE 3.4 4.5 - - - +
691A ILE* 4.2 7.4 - - + -
1001A 90E 3.8 1.8 - - - -
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Residues in contact with LYS 646 (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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625A GLY 6.1 0.2 - - - -
626A GLU 3.3 8.5 - - - +
627A VAL* 4.1 18.2 - - + +
645A ILE* 1.3 73.9 - - - +
647A THR* 1.3 68.2 + - - +
660A PHE* 3.4 27.6 - - + -
663A GLU* 3.3 22.1 + - - +
689A MET* 3.1 4.7 - - - -
690A ILE* 2.9 33.3 + - + +
762A ARG* 3.7 22.4 - - - +
766A ASP* 5.2 1.0 + - - -
1001A 90E 3.5 35.4 - - + +
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Residues in contact with THR 647 (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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615A ARG* 4.0 15.5 - - - +
624A PHE 3.9 0.5 - - - +
625A GLY* 3.4 18.1 - - - -
626A GLU* 2.9 32.8 + - - -
628A TYR* 3.6 26.0 - - + -
645A ILE* 4.4 1.6 - - + -
646A LYS* 1.3 80.7 - - - +
648A LEU* 1.3 62.8 + - - +
649A LYS* 5.1 2.7 + - - +
660A PHE* 3.8 8.5 - - - -
687A PRO* 4.6 9.4 - - + -
688A MET 3.3 7.2 - - - -
689A MET* 4.0 20.9 - - + -
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Residues in contact with LEU 648 (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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624A PHE* 3.5 24.9 - - + +
647A THR* 1.3 75.5 - - - +
649A LYS* 1.3 63.6 + - - +
652A TYR* 3.5 44.9 - - + -
656A GLN* 4.1 16.4 - - + +
657A ARG* 4.1 0.7 - - - -
660A PHE* 3.9 40.6 - - + -
687A PRO* 3.5 17.8 - - - +
688A MET* 3.0 36.2 + - + +
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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