Contacts of the strand formed by residues 687 - 696 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A TYR* 3.1 23.9 + - + +
650A MET* 3.9 9.2 - - + -
651A PRO 3.4 25.4 - - - +
653A THR* 3.6 13.9 - - - +
673A ILE* 3.7 17.3 - - + -
676A LEU* 4.1 21.3 - - + +
677A GLN* 2.9 26.4 + - + -
680A VAL* 3.8 24.2 - - + +
683A ASN* 3.7 32.3 - - + +
685A HIS 3.6 4.9 - - - +
686A PRO* 1.3 76.2 - - - +
688A LEU* 1.3 60.2 + - - +
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Residues in contact with LEU 688 (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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6A TRP* 4.5 8.3 - - + -
11A TYR* 4.6 0.4 - - + -
54A GLN* 5.2 1.3 - - - +
57A LEU* 3.9 34.3 - - + +
58A ALA* 4.0 19.1 - - + +
61A TYR* 3.9 37.0 - - + -
62A LEU* 5.8 0.9 - - + -
653A THR 2.8 11.0 + - - +
654A LEU* 4.0 12.3 - - + -
655A ILE* 2.8 29.6 + - - +
673A ILE* 3.9 3.8 - - - +
677A GLN* 4.7 1.8 - - - +
686A PRO* 3.9 20.0 - - + -
687A LEU* 1.3 80.5 - - - +
689A ILE* 1.3 63.1 + - - +
717A PHE* 4.1 11.7 - - + -
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Residues in contact with ILE 689 (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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50A TRP* 4.7 2.2 - - + -
54A GLN* 3.5 56.8 + - + +
55A ALA* 3.8 0.9 - - - -
58A ALA* 3.7 5.5 - - - +
654A LEU* 4.8 0.2 - - - -
655A ILE* 3.3 19.7 - - + +
657A VAL* 3.8 21.3 - - + -
669A SER* 4.0 19.3 - - - +
670A PHE* 3.8 24.2 - - + -
673A ILE* 3.9 18.4 - - + +
688A LEU* 1.3 77.5 - - - +
690A LYS* 1.3 66.3 + - - +
691A ILE* 3.8 11.1 - - + +
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Residues in contact with LYS 690 (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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55A ALA* 4.7 11.0 - - + +
58A ALA* 4.5 9.4 - - + -
59A GLN* 4.8 9.0 - - + +
62A LEU* 4.2 17.3 - - + -
654A LEU* 4.4 14.3 - - + +
655A ILE 2.8 11.0 + - - +
656A THR* 3.4 18.2 - - + -
657A VAL* 3.0 24.9 + - - +
689A ILE* 1.3 73.6 - - - +
691A ILE* 1.3 66.9 + - - +
706A LYS* 5.3 1.4 - - - +
709A LYS* 4.2 4.2 - - - +
710A ASP* 2.9 30.8 + - - +
713A ASP* 2.7 39.5 + - - +
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Residues in contact with ILE 691 (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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50A TRP* 5.8 0.2 - - + -
51A THR* 3.4 35.7 - - + +
54A GLN* 4.4 0.2 - - + -
55A ALA* 4.0 14.0 - - + +
657A VAL* 3.5 22.2 - - + +
659A ILE* 4.3 9.4 - - + -
670A PHE* 4.0 24.2 - - + -
689A ILE* 3.8 32.3 - - + +
690A LYS* 1.3 84.1 - - - +
692A ASP* 1.3 71.9 + - - +
693A LYS* 3.8 25.5 + - + +
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Residues in contact with ASP 692 (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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657A VAL 2.9 8.9 + - - -
658A ASN* 3.7 9.2 - - - +
659A ILE* 3.3 26.7 + - - +
690A LYS 4.2 0.4 - - - -
691A ILE* 1.3 72.5 - - - +
693A LYS* 1.3 60.2 + - - +
694A SER* 3.0 28.2 + - - +
696A LEU* 6.3 1.3 - - - -
702A LYS* 2.7 42.7 + - - +
706A LYS* 3.0 26.7 + - - +
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Residues in contact with LYS 693 (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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48A ASP* 3.5 11.1 + - - +
51A THR* 2.8 35.5 + - - -
52A THR* 2.9 29.9 + - - +
55A ALA* 6.1 2.0 - - - +
659A ILE* 4.1 14.8 - - + +
691A ILE* 3.8 21.0 + - + +
692A ASP* 1.3 72.6 + - - +
694A SER* 1.3 65.3 + - - +
695A TRP* 3.3 4.2 + - - +
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Residues in contact with SER 694 (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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164A LEU* 3.9 27.4 - - - +
659A ILE* 3.1 19.5 + - - +
692A ASP* 3.0 20.3 + - - +
693A LYS* 1.3 78.6 - - - +
695A TRP* 1.3 59.2 + - - +
696A LEU* 3.1 13.1 + - - +
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Residues in contact with TRP 695 (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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164A LEU* 3.4 8.1 - - - +
165A GLY* 2.8 55.6 + - - -
166A GLY 3.5 9.3 + - - -
167A ASP* 3.2 28.7 + - - -
659A ILE* 3.3 32.8 - - + -
660A GLY* 3.7 21.3 - - - -
661A ALA* 3.5 6.6 - - - +
693A LYS 3.3 3.9 + - - +
694A SER* 1.3 71.7 + - - +
696A LEU* 1.3 63.1 + - - +
225B HIS* 3.3 50.2 - + + +
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Residues in contact with LEU 696 (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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164A LEU* 3.8 18.2 - - + -
658A ASN* 4.3 13.5 - - + +
659A ILE 3.1 15.4 + - - +
660A GLY* 3.2 0.7 - - - -
661A ALA 2.9 26.7 + - - -
663A ARG* 3.5 36.1 - - - +
692A ASP* 6.3 1.1 - - - -
694A SER* 3.1 12.3 + - - +
695A TRP* 1.3 73.4 - - - +
697A GLY* 1.3 62.2 + - - +
700A MET* 4.0 13.5 - - + +
701A GLY* 3.7 25.6 - - - +
702A LYS* 4.4 22.7 - - + +
703A PRO* 6.2 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