Contacts of the strand formed by residues 610 - 617 (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 SER 610 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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598A VAL* 3.9 9.4 - - - -
599A THR 3.6 6.5 - - - -
600A HIS* 2.8 31.3 + - - -
601A PRO* 3.7 4.6 - - - +
608A LYS 4.0 0.6 + - - -
609A PRO* 1.3 74.0 - - - +
611A ILE* 1.3 61.2 + - - +
631A VAL* 3.6 4.0 - - - -
632A GLN* 2.8 36.5 + - - +
633A GLN 3.4 14.8 + - - -
635A ARG* 2.8 19.1 + - - -
636A GLN 4.0 4.9 - - - -
814A ARG* 4.5 0.4 - - - +
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Residues in contact with ILE 611 (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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597A ASP 3.7 0.9 - - - +
598A VAL* 3.2 5.6 - - - -
599A THR* 2.9 39.4 + - - +
609A PRO* 4.5 1.3 - - + +
610A SER* 1.3 78.0 - - - +
612A ALA* 1.3 60.7 + - - +
613A ALA 4.1 0.3 + - - -
629A VAL* 3.7 26.0 - - + -
630A ARG 3.5 6.7 - - - +
631A VAL* 4.8 4.3 - - + -
810A ALA* 3.8 27.2 - - + +
813A ALA* 3.9 3.4 - - + -
814A ARG* 3.6 59.5 - - - +
817A LEU* 3.9 19.5 - - + -
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Residues in contact with ALA 612 (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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597A ASP 3.5 4.7 - - - -
598A VAL* 4.1 12.3 - - + -
610A SER 4.2 1.4 + - - -
611A ILE* 1.3 72.7 - - - +
613A ALA* 1.3 59.3 + - - +
629A VAL* 3.3 5.2 - - - +
630A ARG* 2.9 42.1 + - + +
632A GLN* 3.8 22.8 - - + +
639A ILE* 3.8 24.5 - - + -
645A MET* 3.6 5.9 - - + +
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Residues in contact with ALA 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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595A GLY 3.8 0.6 - - - +
596A ALA* 3.3 3.5 - - - -
597A ASP 2.9 33.4 + - - +
611A ILE 4.1 0.2 + - - -
612A ALA* 1.3 74.4 - - - +
614A VAL* 1.3 65.9 + - - +
628A THR 3.5 4.5 - - - -
629A VAL* 4.5 0.7 - - + -
639A ILE* 4.9 0.2 - - - +
806A ALA* 3.3 28.4 - - - +
809A VAL* 3.5 24.7 - - + -
810A ALA* 3.8 13.0 - - + +
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Residues in contact with VAL 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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594A LEU* 4.4 15.5 - - + -
595A GLY 3.2 11.9 - - - +
596A ALA* 4.2 10.5 - - + -
613A ALA* 1.3 79.9 - - - +
615A VAL* 1.3 67.8 + - - +
627A ALA* 3.6 1.0 - - - -
628A THR* 2.8 47.8 + - - +
639A ILE* 4.2 6.3 - - + -
642A LEU* 3.7 30.1 - - + -
645A MET* 3.7 18.4 - - + -
646A VAL* 5.1 1.3 - - + -
649A LEU* 3.8 19.2 - - + +
666A PHE* 4.8 0.9 - - + -
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Residues in contact with VAL 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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593A PHE 3.7 0.2 - - - +
594A LEU* 3.2 7.6 - - - +
595A GLY 2.8 36.4 + - - +
614A VAL* 1.3 78.7 - - - +
616A GLY* 1.3 58.9 + - - +
625A TYR* 4.1 10.5 - - + -
626A CYS 3.2 9.0 - - - +
627A ALA* 3.7 20.9 - - + -
649A LEU* 4.1 4.3 - - - -
802A PRO* 3.0 38.6 - - + +
805A TYR* 4.0 11.4 - - + -
806A ALA* 4.0 12.1 - - - +
809A VAL* 3.8 16.8 - - + -
858A PHE* 4.9 2.2 - - + -
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Residues in contact with GLY 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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592A ILE* 4.4 0.7 - - - -
593A PHE 3.4 6.7 - - - -
594A LEU* 3.6 14.4 - - - -
615A VAL* 1.3 74.9 - - - +
617A SER* 1.3 67.4 + - - -
618A MET* 3.2 8.3 - - - +
625A TYR* 3.3 5.7 - - - -
626A CYS 3.0 31.3 + - - -
649A LEU* 3.7 9.7 - - - +
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Residues in contact with SER 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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591A VAL 4.3 2.4 + - - -
592A ILE* 3.4 8.8 - - - +
593A PHE* 3.0 34.7 + - - +
616A GLY* 1.3 74.0 - - - -
618A MET* 1.3 64.6 + - - +
619A ASP 4.3 4.7 + - - -
622A PRO* 4.1 18.2 - - - -
624A ARG 3.3 9.2 - - - -
625A TYR* 3.3 26.2 - - - -
653A PHE* 3.2 18.6 - - - -
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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