Contacts of the strand formed by residues 625 - 632 (chain A) in PDB entry 4Z4H
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 TYR 625 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A PHE* 3.7 20.9 - - - +
615A VAL* 4.1 10.3 - - + -
616A GLY 3.3 12.3 - - - -
617A SER* 3.3 35.6 - - - -
618A MET* 4.3 0.9 - - - -
622A PRO* 4.5 11.8 - - - +
623A ASN* 3.2 35.2 - - - -
624A ARG* 1.3 76.5 + - - +
626A CYS* 1.3 68.5 + - - +
786A LEU* 4.7 2.6 - - - +
789A THR* 4.8 2.9 + - - -
801A ALA* 4.8 3.0 - - + +
802A PRO* 3.4 38.7 - - + +
805A TYR* 3.5 30.3 - + + -
854A ARG 5.2 0.3 - - - +
855A THR 4.1 3.8 - - - +
856A MET* 3.1 29.8 - - + +
858A PHE* 4.2 12.7 - - + -
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Residues in contact with CYS 626 (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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615A VAL* 3.2 6.3 - - - +
616A GLY 3.0 31.3 + - - -
618A MET* 3.6 31.8 - - + +
625A TYR* 1.3 75.5 - - - +
627A ALA* 1.3 61.3 + - - +
649A LEU* 3.5 8.6 - - + +
652A GLN* 3.9 18.4 - - + -
656A SER* 5.7 0.2 - - - -
853A LEU 4.3 5.2 - - - +
854A ARG* 3.8 35.4 - - - -
855A THR 4.7 4.3 - - - -
858A PHE* 4.8 0.7 - - - -
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Residues in contact with ALA 627 (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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614A VAL 3.6 4.5 - - - -
615A VAL* 3.7 7.2 - - + -
626A CYS* 1.3 77.3 - - - +
628A THR* 1.3 68.8 + - - +
649A LEU* 4.7 0.4 - - - -
809A VAL* 3.5 36.3 - - + -
848A VAL* 6.0 1.2 - - - +
853A LEU* 4.5 19.5 + - - +
855A THR 4.9 1.0 + - - -
857A TYR* 4.3 14.1 + - + +
858A PHE* 3.8 13.6 - - + -
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Residues in contact with THR 628 (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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613A ALA* 3.5 2.1 - - - -
614A VAL* 2.8 41.0 + - - +
627A ALA* 1.3 80.8 - - - +
629A VAL* 1.3 65.2 + - - +
630A ARG* 4.2 6.7 - - - +
645A MET* 3.3 48.0 + - - +
648A GLU* 3.5 29.8 - - + +
649A LEU* 4.1 10.1 - - + +
809A VAL* 4.0 4.7 - - - +
853A LEU* 6.5 0.2 - - + -
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Residues in contact with VAL 629 (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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611A ILE* 3.7 23.8 - - + -
612A ALA 3.3 13.7 - - - +
613A ALA* 4.5 0.4 - - + -
628A THR* 1.3 78.5 - - - +
630A ARG* 1.3 86.4 + - - +
645A MET* 3.7 0.6 - - - +
809A VAL* 3.9 20.0 - - + +
813A ALA* 3.7 17.0 - - + -
846A VAL* 3.6 33.3 - - + +
847A GLN* 5.4 2.8 - - - +
848A VAL* 5.8 2.0 - - + -
857A TYR* 4.6 9.4 - - - +
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Residues in contact with ARG 630 (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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611A ILE* 3.5 8.1 - - - +
612A ALA* 2.9 37.4 + - + +
628A THR* 4.2 7.7 - - - +
629A VAL* 1.3 101.4 + - - +
631A VAL* 1.3 70.1 + - - +
632A GLN* 5.7 2.0 - - + +
641A ASP* 3.2 33.8 + - + +
644A ALA* 4.2 8.9 - - - +
645A MET* 3.7 30.8 - - + +
648A GLU* 2.5 31.3 + - - -
843A ALA* 6.6 0.2 - - - -
846A VAL* 4.8 4.0 - - - -
847A GLN* 5.0 8.2 + - - -
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Residues in contact with VAL 631 (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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609A PRO* 4.3 15.0 - - + -
610A SER 3.6 4.3 - - - -
611A ILE* 4.7 3.6 - - + +
630A ARG* 1.3 82.9 - - - +
632A GLN* 1.3 61.4 + - - +
817A LEU* 4.0 16.6 - - + -
839A HIS* 3.3 35.1 - - + +
842A LEU* 3.9 18.2 - - + +
843A ALA* 3.9 23.5 - - + +
846A VAL* 3.9 29.0 - - + +
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Residues in contact with GLN 632 (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 VAL* 4.2 8.9 - - - +
609A PRO* 3.5 9.3 - - - +
610A SER* 2.8 39.1 + - - +
612A ALA* 3.8 18.7 - - + +
630A ARG* 5.4 2.2 - - + +
631A VAL* 1.3 75.8 - - - +
633A GLN* 1.3 68.8 + - - +
634A HIS 3.5 0.2 + - - -
636A GLN* 2.7 34.6 + - - +
637A GLU 4.2 0.2 - - - -
638A ILE 2.9 20.5 + - - -
639A ILE* 3.5 4.2 - - - +
640A GLN* 2.9 36.9 + - + +
641A ASP 4.8 0.5 + - - -
839A HIS* 4.8 7.6 - - - -
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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