Contacts of the strand formed by residues 663 - 669 (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 ARG 663 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585A PRO 5.3 0.6 + - - -
586A VAL* 4.0 39.9 + - - +
588A GLN* 6.3 0.2 - - - +
589A GLN* 3.3 35.3 + - - +
590A PRO 3.5 1.6 + - - +
591A VAL* 3.6 16.7 - - + -
592A ILE 3.2 22.9 + - - -
661A PRO* 3.2 8.6 - - - +
662A THR* 1.3 89.9 + - - +
664A ILE* 1.3 64.9 + - - +
665A ILE* 4.7 2.5 - - + -
700A PRO* 4.2 0.2 - - - -
701A GLY 3.3 8.7 - - - +
772A ASN* 3.1 44.4 + - - +
774A PHE* 5.5 0.2 - - - -
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Residues in contact with ILE 664 (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* 3.8 22.0 - - + -
594A LEU* 4.2 23.8 - - + -
646A VAL* 5.3 2.0 - - + -
650A LEU* 4.4 14.4 - - + -
661A PRO* 4.7 3.4 - - + -
663A ARG* 1.3 79.0 - - - +
665A ILE* 1.3 67.4 + - - +
666A PHE* 3.9 5.8 + - + +
687A ILE* 4.0 21.3 - - + -
691A CYS* 3.8 17.5 - - - -
700A PRO* 3.6 27.8 - - + -
701A GLY 2.7 11.7 + - - +
702A ILE* 3.4 8.7 - - + +
703A THR 2.9 26.9 + - - +
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Residues in contact with ILE 665 (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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586A VAL* 4.8 2.2 - - + -
591A VAL* 3.8 19.7 - - + -
592A ILE 3.1 4.6 + - - -
593A PHE* 3.5 31.3 - - + +
594A LEU* 2.7 33.6 + - - +
663A ARG* 4.7 3.1 - - + -
664A ILE* 1.3 79.0 - - - +
666A PHE* 1.3 56.1 + - - +
667A TYR* 3.8 26.2 + - + -
703A THR* 3.7 11.7 - - + +
705A ILE* 4.1 15.9 - - + -
772A ASN* 4.3 6.7 - - - +
774A PHE* 4.0 29.8 - - + -
779A LEU* 5.4 0.7 - - + -
782A LEU* 4.5 7.4 - - + -
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Residues in contact with PHE 666 (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* 3.5 31.6 - - + -
596A ALA* 3.7 26.9 - - + -
614A VAL* 4.8 1.3 - - + -
642A LEU* 4.0 30.3 - - + -
664A ILE* 4.8 4.9 - - + +
665A ILE* 1.3 73.4 - - - +
667A TYR* 1.3 61.5 + - - +
668A ARG* 3.6 17.9 - - + -
683A GLU* 4.1 4.0 - - - -
687A ILE* 3.7 25.6 - - + -
702A ILE* 5.1 1.3 - - + -
703A THR 2.9 14.4 + - - +
704A PHE* 3.3 42.2 - + - -
705A ILE* 2.9 29.6 + - - +
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Residues in contact with TYR 667 (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* 4.6 1.8 - + - -
594A LEU 2.8 17.6 + - - +
595A GLY* 3.6 2.9 - - - -
596A ALA 3.1 23.0 + - - +
665A ILE* 3.8 18.6 - - + -
666A PHE* 1.3 73.9 - - - +
668A ARG* 1.3 60.9 + - - +
669A ASP 3.8 1.4 + - - -
705A ILE* 3.4 34.4 - - + +
707A VAL* 3.8 24.2 - - + -
765A TYR* 4.3 1.1 - + - -
779A LEU* 4.4 0.2 - - - +
782A LEU* 4.2 8.0 - - - +
783A THR* 2.8 38.8 + - + -
786A LEU* 3.5 27.7 - - + +
800A PRO* 3.9 19.3 - - + -
802A PRO* 4.4 11.2 - - + -
803A ALA* 4.6 14.0 - - + +
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Residues in contact with ARG 668 (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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596A ALA* 3.9 18.4 - - - -
597A ASP* 4.2 2.8 - - - +
598A VAL* 3.9 11.7 - - - +
637A GLU* 2.7 55.7 + - - +
639A ILE* 3.8 10.6 - - - +
666A PHE* 3.6 14.3 + - + -
667A TYR* 1.3 72.8 - - - +
669A ASP* 1.3 76.7 + - - +
670A GLY 3.7 0.7 + - - -
671A VAL* 3.8 19.8 - - + +
679A VAL* 4.1 2.4 - - - +
683A GLU* 2.8 38.6 + - - +
704A PHE* 4.0 13.7 - - + -
705A ILE 2.6 15.6 + - - +
706A VAL* 3.2 7.1 - - + +
707A VAL* 2.7 25.1 + - - +
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Residues in contact with ASP 669 (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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596A ALA 3.0 18.4 + - - +
597A ASP* 3.0 25.7 - - + +
637A GLU* 4.0 1.2 - - - +
667A TYR 3.8 1.6 + - - -
668A ARG* 1.3 94.5 + - - +
670A GLY* 1.3 67.6 + - - +
671A VAL 3.6 0.9 - - - -
707A VAL* 3.4 20.2 - - + +
709A LYS* 4.9 10.4 + - - +
799A ILE* 4.5 8.5 - - - +
803A ALA* 4.7 11.9 - - + +
807A HIS* 3.0 31.4 + - + +
901A MG 4.0 2.3 - - - -
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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