Contacts of the strand formed by residues 613 - 620 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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605A ASN* 4.6 19.3 - - - +
606A LEU 3.3 6.0 - - - -
607A LYS* 3.8 21.8 + - - +
608A GLN* 4.8 0.2 - - - -
611A GLY 4.1 0.5 + - - -
612A THR* 1.3 81.1 + - - +
614A LEU* 1.3 60.8 + - - +
615A LYS 4.3 0.5 + - - -
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Residues in contact with LEU 614 (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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605A ASN* 3.3 5.5 - - - -
606A LEU* 2.8 41.6 + - + +
608A GLN* 3.6 35.4 - - + +
612A THR 4.2 0.2 + - - -
613A SER* 1.3 76.0 - - - +
615A LYS* 1.3 78.5 + - + +
616A VAL* 3.4 6.5 + - + +
651A ARG* 4.2 22.9 - - - +
653A LEU* 3.7 30.5 - - + -
672A PRO* 4.9 4.0 - - + -
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Residues in contact with LYS 615 (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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603A GLU* 2.6 37.4 + - - -
604A GLY* 3.1 14.2 + - - +
605A ASN* 2.7 25.0 + - - +
613A SER 4.3 0.8 + - - -
614A LEU* 1.3 83.2 - - - +
616A VAL* 1.3 64.8 + - - +
672A PRO* 3.9 0.5 - - - +
673A PHE* 3.0 48.4 + - + +
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Residues in contact with VAL 616 (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 LEU* 3.9 16.8 - - + -
603A GLU* 3.6 5.2 - - - +
604A GLY 2.8 47.4 + - - +
606A LEU* 3.9 13.0 - - + +
614A LEU* 3.8 11.2 - - + +
615A LYS* 1.3 81.5 - - - +
617A ALA* 1.3 60.3 + - - +
618A VAL* 4.0 6.5 - - + -
653A LEU* 3.6 31.0 - - + -
670A ILE* 3.7 21.5 - - + -
671A LEU 3.2 8.3 - - - +
673A PHE* 3.5 11.3 - - - +
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Residues in contact with ALA 617 (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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1A ANP 3.5 46.2 - - + +
593A LEU* 4.0 13.7 - - + -
601A VAL* 4.6 3.4 - - + -
602A MET 3.3 4.3 - - - -
616A VAL* 1.3 75.0 - - - +
618A VAL* 1.3 63.4 + - - +
619A LYS 4.1 0.7 - - - -
669A VAL 3.5 1.7 - - - +
670A ILE* 3.8 0.3 - - - -
671A LEU* 2.7 41.5 + - + +
673A PHE* 3.8 2.1 - - + +
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Residues in contact with VAL 618 (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 LEU* 4.1 9.2 - - + -
589A LEU* 3.7 33.9 - - + -
600A SER 3.5 2.6 - - - +
601A VAL* 3.1 4.9 - - - -
602A MET* 2.8 44.8 + - + +
604A GLY 4.9 2.5 - - - +
616A VAL* 4.0 21.1 - - + -
617A ALA* 1.3 78.2 - - - +
619A LYS* 1.3 61.5 + - - +
620A THR* 3.9 3.5 + - + -
668A MET* 3.8 34.3 - - + -
669A VAL 3.4 5.4 - - - +
670A ILE* 4.3 9.2 - - + -
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Residues in contact with LYS 619 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A ANP 4.8 14.1 - - - +
600A SER 3.6 4.0 - - - +
601A VAL* 4.0 22.0 - - + -
617A ALA 4.1 0.2 - - - -
618A VAL* 1.3 72.5 - - - +
620A THR* 1.3 64.3 + - - +
621A MET* 4.2 16.7 - - + +
668A MET* 3.4 1.1 - - - -
669A VAL* 2.8 49.7 + - + +
671A LEU* 4.2 18.4 - - + +
741A ASP* 3.8 26.2 - - - +
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Residues in contact with THR 620 (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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598A PHE 3.8 11.2 + - - +
599A GLY* 3.9 8.5 + - - -
600A SER* 2.9 34.7 + - - +
602A MET* 3.7 29.4 - - + -
618A VAL* 4.7 1.6 - - + -
619A LYS* 1.3 76.0 - - - +
621A MET* 1.3 70.0 + - - +
667A PRO 3.6 7.6 - - - -
668A MET* 3.6 24.2 - - + -
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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