Contacts of the strand formed by residues 613 - 620 (chain B) in PDB entry 2P0C
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 SER 613 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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605B ASN* 5.1 12.1 - - - -
606B LEU 3.2 9.9 - - - -
607B LYS* 4.2 15.6 - - - +
608B GLN* 4.5 1.9 + - - -
611B GLY 4.9 1.4 + - - -
612B THR* 1.3 79.3 + - - +
614B LEU* 1.3 63.2 + - - +
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Residues in contact with LEU 614 (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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605B ASN* 3.4 4.7 - - - -
606B LEU* 2.8 36.0 + - + +
608B GLN* 3.7 34.1 - - + +
612B THR 4.2 0.2 + - - -
613B SER* 1.3 75.9 - - - +
615B LYS* 1.3 73.6 + - - +
616B VAL* 3.6 3.8 + - + +
653B LEU* 3.8 31.6 - - + -
672B PRO* 5.0 8.7 - - + -
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Residues in contact with LYS 615 (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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603B GLU* 3.0 36.8 + - - -
604B GLY 3.4 9.1 + - - +
605B ASN* 3.0 25.3 + - - +
614B LEU* 1.3 84.6 - - - +
616B VAL* 1.3 64.9 + - - +
672B PRO* 3.9 0.3 - - - +
673B PHE* 2.9 48.4 + - + +
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Residues in contact with VAL 616 (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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587B LEU* 3.8 22.4 - - + -
603B GLU* 3.4 4.9 - - - +
604B GLY* 2.7 59.5 + - - +
605B ASN 3.7 5.6 - - - +
606B LEU* 3.8 14.1 - - + -
614B LEU* 3.9 4.0 - - + +
615B LYS* 1.3 80.7 - - - +
617B ALA* 1.3 57.6 + - - +
618B VAL* 3.9 6.5 - - + -
653B LEU* 3.6 17.3 - - + -
670B ILE* 3.6 21.5 - - + -
671B LEU 3.2 13.7 - - - +
673B PHE* 3.6 9.7 - - - +
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Residues in contact with ALA 617 (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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2B ANP 3.4 49.4 - - + +
593B LEU* 4.8 1.3 - - + -
601B VAL* 4.6 7.9 - - + -
602B MET 3.4 6.7 - - - +
616B VAL* 1.3 72.3 - - - +
618B VAL* 1.3 61.1 + - - +
619B LYS 4.1 0.2 + - - -
669B VAL 3.4 3.1 - - - +
670B ILE* 3.9 1.4 - - - -
671B LEU* 2.9 38.0 + - + +
673B PHE* 3.9 6.7 - - + +
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Residues in contact with VAL 618 (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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587B LEU* 3.9 11.9 - - + -
589B LEU* 3.8 33.2 - - + -
600B SER 3.8 1.4 - - - +
601B VAL* 3.2 5.0 - - - -
602B MET* 2.6 50.2 + - + +
604B GLY* 4.6 3.6 - - - -
616B VAL* 3.9 21.8 - - + -
617B ALA* 1.3 76.1 - - - +
619B LYS* 1.3 63.5 + - - +
620B THR 4.1 0.2 + - - -
668B MET* 3.7 33.0 - - + -
669B VAL 3.5 2.2 - - - -
670B ILE* 3.8 11.4 - - + -
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Residues in contact with LYS 619 (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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2B ANP 4.7 16.2 - - + +
600B SER 3.8 7.4 - - - +
601B VAL* 4.4 13.7 - - + +
617B ALA 4.1 0.4 + - - -
618B VAL* 1.3 74.3 - - - +
620B THR* 1.3 66.7 + - - +
621B MET* 3.8 32.8 - - + +
668B MET* 3.3 2.9 - - - -
669B VAL* 2.8 53.4 + - + +
671B LEU* 4.8 10.1 - - + -
741B ASP* 4.7 12.1 - - - +
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Residues in contact with THR 620 (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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599B GLY* 3.9 19.1 + - - -
600B SER* 2.9 32.4 + - - +
602B MET* 3.7 27.4 - - + -
618B VAL* 4.9 0.4 - - + -
619B LYS* 1.3 73.1 - - - +
621B MET* 1.3 71.2 + - - +
666B LYS* 5.9 6.5 - - + -
667B PRO 3.6 5.6 - - - -
668B MET* 3.7 25.1 - - + +
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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