Contacts of the strand formed by residues 635 - 642 (chain B) in PDB entry 5M9N
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 ILE 635 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496B CYS* 3.5 3.2 - - - -
497B GLY* 2.8 35.1 + - - +
499B VAL* 4.2 11.2 - - + +
629B LEU 4.3 1.3 - - - +
630B VAL* 4.2 30.1 - - + -
633B LYS* 3.7 27.6 - - + +
634B ILE* 1.3 75.7 - - - +
636B THR* 1.3 76.7 + - - +
637B VAL* 3.7 4.7 + - + +
651B LEU* 3.9 24.0 - - + -
652B ILE 3.7 11.2 - - - +
653B ASP* 3.9 29.4 - - + +
662B VAL* 5.4 2.5 - - + -
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Residues in contact with THR 636 (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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494B GLU* 4.0 22.9 - - + +
495B PHE 3.6 11.4 - - - +
496B CYS* 4.2 13.6 - - - +
634B ILE 4.3 0.6 + - - -
635B ILE* 1.3 70.2 - - - +
637B VAL* 1.3 67.5 + - - +
638B LYS* 4.0 1.0 + - + -
650B GLU 3.5 1.9 - - - +
651B LEU* 3.5 3.1 - - - -
652B ILE* 2.7 53.7 + - + +
654B LYS* 3.3 38.2 - - - +
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Residues in contact with VAL 637 (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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493B ASP 3.9 0.5 - - - +
494B GLU* 3.3 5.0 - - - +
495B PHE* 2.9 71.7 + - + +
497B GLY* 4.8 4.9 - - - +
499B VAL* 5.3 0.7 - - + -
510B CYS* 4.1 15.7 - - + -
606B CYS* 5.2 0.2 - - - -
635B ILE* 4.2 13.5 - - + +
636B THR* 1.3 74.6 - - - +
638B LYS* 1.3 63.0 + - - +
649B VAL* 3.6 31.9 - - + -
650B GLU 3.4 2.9 - - - +
651B LEU* 3.8 19.1 - - + -
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Residues in contact with LYS 638 (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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492B GLY* 4.9 14.1 - - - -
493B ASP 3.6 4.0 - - - +
494B GLU* 3.8 31.0 + - + +
636B THR* 4.0 1.5 + - + -
637B VAL* 1.3 75.5 - - - +
639B VAL* 1.3 65.3 + - - +
640B VAL* 3.4 18.9 + - + -
649B VAL* 3.2 6.0 - - - -
650B GLU* 2.9 67.3 + - + +
652B ILE* 4.8 7.2 - - + -
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Residues in contact with VAL 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B LEU* 4.1 28.7 - - + -
490B ASN 3.6 25.4 - - - +
491B VAL* 4.1 7.6 - - - +
492B GLY* 2.8 32.7 + - - -
493B ASP* 2.9 16.9 + - + +
495B PHE* 4.5 8.7 - - + -
638B LYS* 1.3 72.5 - - - +
640B VAL* 1.3 60.3 + - - +
641B ASP 3.8 18.2 - - - +
642B LYS* 4.3 11.9 - - + -
647B SER* 4.4 6.5 - - - +
648B LEU 3.7 5.6 - - - +
649B VAL* 4.1 11.0 - - + -
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Residues in contact with VAL 640 (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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491B VAL* 3.8 17.3 - - - +
609B ALA* 3.5 29.6 - - + -
638B LYS* 3.9 17.3 - - + +
639B VAL* 1.3 76.4 - - - +
641B ASP* 1.3 66.4 + - - +
648B LEU* 2.9 24.3 + - + +
649B VAL 4.2 0.4 - - - +
650B GLU* 3.5 35.2 - - + +
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Residues in contact with ASP 641 (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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491B VAL* 3.8 9.5 - - - +
639B VAL* 3.8 5.7 - - - +
640B VAL* 1.3 80.4 - - - +
642B LYS* 1.3 91.2 + - - +
643B LEU* 5.5 4.5 - - + -
647B SER* 3.7 4.0 - - - -
648B LEU* 2.9 54.7 + - + +
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Residues in contact with LYS 642 (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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487B LEU 5.3 2.6 + - - -
489B LEU* 2.9 39.8 + - - +
490B ASN* 4.8 0.4 - - - -
491B VAL* 4.0 15.4 - - + +
639B VAL* 4.3 10.1 - - + -
641B ASP* 1.3 95.1 + - - +
643B LEU* 1.3 68.6 + - - +
646B SER 4.1 5.1 + - - -
647B SER* 3.7 18.7 + - - +
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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