Contacts of the strand formed by residues 687 - 696 (chain B) in PDB entry 5N4D
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 LEU 687 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B TYR* 3.2 22.1 + - + +
650B MET* 3.9 9.9 - - + -
651B PRO 3.5 24.7 - - - +
653B THR* 3.6 14.1 - - - +
673B ILE* 3.6 16.8 - - + -
676B LEU* 4.0 23.3 - - + +
677B GLN* 2.9 27.8 + - + +
680B VAL* 3.7 31.9 - - + +
683B ASN* 3.8 21.8 - - + +
685B HIS 3.7 5.2 - - - +
686B PRO* 1.3 76.7 - - - +
688B LEU* 1.3 60.6 + - - +
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Residues in contact with LEU 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TRP* 4.6 4.7 - - + +
11B TYR* 4.4 3.6 - - + -
54B GLN* 5.3 1.1 - - - +
57B LEU* 3.8 34.5 - - + +
58B ALA* 4.0 16.2 - - + +
61B TYR* 3.9 31.2 - - + -
62B LEU* 6.0 0.9 - - + -
653B THR 2.9 9.7 + - - +
654B LEU* 3.9 14.8 - - + -
655B ILE* 2.9 29.5 + - - +
673B ILE* 3.7 4.8 - - - +
677B GLN* 4.7 2.0 - - - +
686B PRO* 3.8 27.4 - - + -
687B LEU* 1.3 84.3 - - - +
689B ILE* 1.3 60.1 + - - +
717B PHE* 4.0 12.3 - - + -
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Residues in contact with ILE 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TRP* 4.8 1.1 - - + -
54B GLN* 3.4 55.0 + - + +
55B ALA* 3.7 4.5 - - - -
58B ALA* 3.6 7.9 - - - +
654B LEU* 4.6 0.2 - - - -
655B ILE* 3.3 20.6 - - + +
657B VAL* 3.9 20.9 - - + -
669B SER 4.0 7.0 - - - +
670B PHE* 3.9 24.9 - - + -
673B ILE* 3.9 27.6 - - + -
688B LEU* 1.3 76.8 - - - +
690B LYS* 1.3 63.8 + - - +
691B ILE* 4.0 13.1 - - + +
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Residues in contact with LYS 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ALA* 4.8 8.7 - - + +
58B ALA* 4.5 10.8 - - + -
59B GLN* 5.2 7.2 - - + +
62B LEU* 4.2 17.5 - - + -
654B LEU* 4.4 12.3 - - + +
655B ILE 2.8 10.2 + - - +
656B THR* 3.4 21.0 - - + -
657B VAL* 3.0 25.1 + - - +
689B ILE* 1.3 73.7 - - - +
691B ILE* 1.3 64.1 + - - +
706B LYS* 5.5 0.2 - - - +
709B LYS* 4.6 2.5 - - - +
710B ASP* 3.0 33.9 + - - +
713B ASP* 3.1 34.7 + - + +
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Residues in contact with ILE 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TRP* 5.5 0.2 - - + -
51B THR* 3.5 36.6 - - + +
55B ALA* 4.1 12.8 - - + +
657B VAL* 3.6 20.4 - - + +
659B ILE* 4.4 9.0 - - + -
670B PHE* 3.9 24.9 - - + -
689B ILE* 4.0 32.1 - - + +
690B LYS* 1.3 82.8 - - - +
692B ASP* 1.3 70.7 + - - +
693B LYS* 3.8 25.2 + - + +
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Residues in contact with ASP 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657B VAL 2.9 9.3 + - - -
658B ASN* 3.7 10.8 - - - +
659B ILE* 3.3 25.1 + - - +
690B LYS 4.2 0.2 - - - -
691B ILE* 1.3 71.2 - - - +
693B LYS* 1.3 65.0 + - - +
694B SER* 3.0 25.5 + - - +
696B LEU* 6.2 1.9 - - - +
702B LYS* 2.9 42.6 + - - +
706B LYS* 3.0 24.8 + - - +
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Residues in contact with LYS 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ASP* 3.6 11.3 + - - +
51B THR* 2.9 33.1 + - - -
52B THR* 2.8 33.1 + - - +
55B ALA* 6.0 2.0 - - - -
659B ILE* 4.2 13.9 - - + +
691B ILE* 3.8 21.7 + - + +
692B ASP* 1.3 75.4 + - - +
694B SER* 1.3 64.8 + - - +
695B TRP* 3.3 3.5 + - - +
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Residues in contact with SER 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B LEU* 3.8 28.6 - - - +
659B ILE* 3.0 19.3 + - - +
692B ASP* 3.0 21.4 + - - +
693B LYS* 1.3 76.5 - - - +
695B TRP* 1.3 57.9 + - - +
696B LEU* 3.0 13.1 + - - +
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Residues in contact with TRP 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A HIS* 3.2 51.4 - + + +
164B LEU* 3.4 9.7 - - - +
165B GLY* 2.9 48.3 + - - +
166B GLY 3.5 7.1 + - - -
167B ASP* 3.1 28.4 + - - -
229B ARG* 3.4 32.1 - - - -
659B ILE* 3.3 33.2 - - + -
660B GLY* 3.9 11.9 - - - -
661B ALA 3.4 11.9 - - - +
693B LYS 3.3 4.3 + - - +
694B SER* 1.3 71.2 + - - +
696B LEU* 1.3 69.1 + - - +
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Residues in contact with LEU 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU* 3.8 17.3 - - + -
658B ASN* 4.3 13.9 - - + +
659B ILE 3.0 17.5 + - - +
660B GLY* 3.1 0.9 - - - -
661B ALA 2.9 26.5 + - - -
663B ARG* 3.6 35.7 - - - +
692B ASP* 6.0 1.6 - - - +
694B SER* 3.0 11.6 + - - +
695B TRP* 1.3 74.2 - - - +
697B GLY* 1.3 62.0 + - - +
700B MET* 3.9 13.9 - - + +
701B GLY* 3.7 26.9 - - - +
702B LYS* 4.3 21.8 - - + +
703B PRO* 6.1 0.2 - - + -
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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