Contacts of the strand formed by residues 652 - 660 (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 ALA 652 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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596A GLY 4.0 5.2 + - - +
597A ALA* 3.2 3.5 - - - +
598A ALA 2.8 25.8 + - - +
651A PRO* 1.3 70.7 - - - +
653A THR* 1.3 57.8 + - - +
685A HIS* 3.4 22.3 - - + +
686A PRO* 3.4 17.0 - - + -
717A PHE* 3.7 16.0 - - + -
721A ALA* 3.6 30.5 - - + -
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Residues in contact with THR 653 (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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587A ILE* 3.8 24.3 - - + +
598A ALA* 3.2 16.7 - - + +
600A PRO* 4.0 8.5 - - + -
651A PRO 2.8 20.1 + - - -
652A ALA* 1.3 72.4 + - - +
654A LEU* 1.3 62.5 + - - +
655A ILE* 3.7 29.2 - - + -
672A PHE* 5.5 0.7 - - + -
673A ILE* 5.2 1.1 - - + -
676A LEU* 4.8 5.6 - - + -
686A PRO 2.9 9.9 + - - +
687A LEU* 3.8 14.9 - - - +
688A LEU* 2.8 28.3 + - - +
717A PHE* 3.7 6.0 - - - -
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Residues in contact with LEU 654 (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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58A ALA* 4.4 7.6 - - + -
62A LEU* 4.7 12.8 - - + -
598A ALA 3.0 8.2 + - - -
599A VAL* 3.3 30.5 - - + +
653A THR* 1.3 74.5 - - - +
655A ILE* 1.3 67.1 + - - +
656A THR* 4.1 17.9 - - + -
688A LEU* 3.6 26.2 - - + +
690A LYS* 4.4 17.0 - - + -
713A ASP* 4.4 11.7 - - + +
714A LYS* 4.4 10.3 - - - +
717A PHE* 3.6 41.6 - - + -
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Residues in contact with ILE 655 (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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584A MET* 4.6 3.6 - - + -
600A PRO* 3.5 30.5 - - + +
653A THR* 3.7 14.4 - - + -
654A LEU* 1.3 72.1 - - - +
656A THR* 1.3 66.1 + - - +
657A VAL* 4.4 0.2 - - + -
669A SER* 3.7 34.1 - - - +
672A PHE* 3.8 29.2 - - + -
673A ILE* 3.8 29.8 - - + +
688A LEU 2.8 15.5 + - - +
689A ILE* 3.3 11.0 - - + +
690A LYS* 2.8 26.7 + - - +
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Residues in contact with THR 656 (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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599A VAL* 4.4 8.7 - - + -
600A PRO 3.1 6.5 + - - +
601A GLU* 3.2 28.2 - - - +
602A GLY 2.8 27.7 + - - -
654A LEU* 4.1 26.0 - - + +
655A ILE* 1.3 79.5 - - - +
657A VAL* 1.3 65.5 + - - +
658A ASN* 4.3 2.9 + - - -
690A LYS* 3.4 20.0 - - + -
714A LYS* 5.7 4.9 - - + -
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Residues in contact with VAL 657 (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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602A GLY* 4.6 6.1 - - - +
655A ILE* 4.4 0.7 - - + -
656A THR* 1.3 79.6 - - - +
658A ASN* 1.3 73.1 + - - +
659A ILE* 4.1 3.4 - - + -
664A VAL 6.1 0.2 - - - +
666A PRO* 3.6 29.2 - - + -
669A SER* 3.5 33.4 - - - +
670A PHE* 4.5 2.5 - - + -
689A ILE* 3.8 17.9 - - + -
690A LYS 3.0 10.6 + - - +
691A ILE* 4.1 18.2 - - + -
692A ASP* 2.9 27.4 + - - +
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Residues in contact with ASN 658 (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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602A GLY* 5.3 5.0 - - - -
656A THR* 5.9 2.6 + - - -
657A VAL* 1.3 85.3 + - - +
659A ILE* 1.3 63.9 + - - +
660A GLY 4.2 0.2 + - - -
663A ARG* 3.8 36.5 - - - +
664A VAL 4.9 4.9 - - - +
666A PRO* 5.6 0.9 - - - +
692A ASP* 3.7 6.6 - - + +
696A LEU* 4.3 8.9 - - + +
702A LYS* 2.8 41.7 + - - +
12C GLU* 3.5 23.4 + - - -
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Residues in contact with ILE 659 (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* 4.1 7.4 - - + -
658A ASN* 1.3 74.7 - - - +
660A GLY* 1.3 58.6 + - - +
663A ARG* 4.1 2.7 - - - -
666A PRO* 3.6 39.0 - - + -
670A PHE* 5.1 2.0 - - + -
691A ILE* 4.3 11.9 - - + -
692A ASP 3.3 21.0 + - - +
693A LYS* 4.1 16.6 - - + +
694A SER 3.1 19.0 + - - +
695A TRP* 3.3 40.2 - - + -
696A LEU* 3.1 14.2 + - - +
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Residues in contact with GLY 660 (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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659A ILE* 1.3 80.8 - - - +
661A ALA* 1.3 68.2 + - - -
662A GLY 3.4 0.5 + - - -
663A ARG* 3.3 25.6 + - - +
695A TRP* 3.7 22.1 - - - -
696A LEU 3.2 15.5 - - - -
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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