Contacts of the strand formed by residues 612 - 618 (chain A) in PDB entry 3ZRH
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 VAL 612 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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594A ASN* 3.7 10.4 - - - +
611A ASP* 1.3 90.0 + - - +
613A THR* 1.3 73.6 + - - +
614A ILE* 3.8 24.6 + - + +
666A LYS* 4.5 10.8 - - + -
667A SER 3.4 15.7 - - - +
668A SER* 4.8 10.1 - - - +
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Residues in contact with THR 613 (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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382A THR* 4.8 3.3 + - - +
592A MET 5.3 0.7 - - - -
593A GLU* 3.6 22.5 - - + +
594A ASN* 2.7 46.9 - - + +
611A ASP 4.0 3.1 + - - +
612A VAL* 1.3 75.6 - - - +
614A ILE* 1.3 62.3 + - - +
615A THR* 4.0 5.6 - - - -
665A GLN 3.5 2.1 - - - +
666A LYS* 3.3 4.5 - - - -
667A SER* 2.7 60.3 + - - +
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Residues in contact with ILE 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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428A LEU 4.6 2.9 - - - +
429A ASP 5.6 0.5 - - - +
430A SER* 3.8 7.4 + - - -
594A ASN* 3.2 18.9 + - - +
612A VAL* 3.8 24.2 - - + +
613A THR* 1.3 73.2 - - - +
615A THR* 1.3 63.8 + - - +
616A PHE* 3.7 41.7 - - + -
664A MET* 3.8 24.7 - - + -
665A GLN 3.7 1.1 - - - -
666A LYS* 3.6 27.6 - - + -
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Residues in contact with THR 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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382A THR* 5.4 3.6 - - - +
430A SER* 3.5 14.3 - - - +
432A LEU* 4.2 3.1 - - + -
591A ALA* 3.5 34.2 - - + +
592A MET 5.0 3.1 + - - -
613A THR* 5.1 5.9 - - - -
614A ILE* 1.3 74.3 + - - +
616A PHE* 1.3 63.9 + - - +
617A LEU* 3.6 23.1 + - + -
663A ALA 3.5 0.9 - - - +
664A MET* 3.4 4.7 - - - -
665A GLN* 2.8 60.6 + - - +
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Residues in contact with PHE 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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424A LEU* 4.1 20.3 - - + +
428A LEU* 3.7 40.2 - - + -
430A SER* 2.8 35.2 + - - +
432A LEU* 5.6 0.2 - - - +
614A ILE* 3.7 25.8 - - + -
615A THR* 1.3 72.7 - - - +
617A LEU* 1.3 64.6 + - - +
618A PRO* 3.8 6.6 - - - +
654A CYS* 4.0 10.8 - - - -
656A THR* 5.7 0.7 - - + -
662A VAL* 3.9 23.8 - - + -
663A ALA 3.6 2.0 - - - -
664A MET* 3.6 35.4 - - + -
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Residues in contact with LEU 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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432A LEU* 3.6 42.6 - - + -
538A ILE* 4.1 11.9 - - + -
540A TYR* 3.4 11.4 - - - +
576A PRO* 3.9 27.6 - - + +
577A ILE 4.9 0.7 - - - -
578A ALA* 4.3 20.4 - - + -
615A THR* 4.1 15.9 - - + +
616A PHE* 1.3 75.0 - - - +
618A PRO* 1.3 67.2 - - - +
619A LEU* 4.2 0.2 - - - +
662A VAL* 3.2 2.5 - - - +
663A ALA* 2.7 43.4 + - - +
665A GLN* 4.4 17.7 - - + +
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Residues in contact with PRO 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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417A ILE 6.1 0.2 - - - +
418A ILE* 6.5 0.7 - - - -
419A ASN 6.3 0.9 - - - +
420A TRP* 4.0 22.2 - - + +
424A LEU* 3.8 26.7 - - + -
432A LEU* 5.3 4.9 - - + -
540A TYR* 2.8 49.7 + - + +
616A PHE 3.8 2.0 - - - +
617A LEU* 1.3 87.4 - - + +
619A LEU* 1.3 62.8 + - - +
620A VAL 3.3 18.6 - - - +
627A LEU* 3.9 2.6 - - - +
660A VAL* 4.3 4.5 - - + -
661A LEU 3.6 6.5 - - - +
662A VAL* 3.8 4.7 - - + -
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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