Contacts of the strand formed by residues 698 - 708 (chain A) in PDB entry 4Z96
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 698 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579A GLN* 3.3 12.6 - - - -
691A MET 3.9 0.3 - - - +
692A TYR* 3.4 5.8 - - - -
693A ASP* 3.1 31.3 + - - +
696A THR* 2.7 27.6 + - - -
697A ARG* 1.3 79.7 - - - +
699A LEU* 1.3 66.3 + - - +
700A ASN* 3.4 16.0 + - - -
786A TYR* 5.4 0.2 - - - -
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Residues in contact with LEU 699 (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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577A GLY* 4.8 4.3 - - - -
578A HIS 4.0 13.4 - - - +
579A GLN* 3.0 54.1 + - - +
580A GLY 4.0 5.4 - - - +
690A LYS* 4.2 27.4 - - + -
691A MET 3.6 11.7 - - - +
692A TYR* 4.1 19.3 - - + -
698A SER* 1.3 76.1 - - - +
700A ASN* 1.3 68.5 + - - +
701A TYR 4.2 0.2 - - - -
767A VAL* 4.5 4.3 - - + -
786A TYR* 3.6 19.3 + - + -
787A PHE* 3.8 24.5 - - + -
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Residues in contact with ASN 700 (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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577A GLY* 5.6 2.4 - - - +
690A LYS* 3.8 1.7 - - - -
691A MET* 2.9 61.9 + - + +
693A ASP* 4.3 4.5 - - - +
698A SER* 3.4 24.0 + - - +
699A LEU* 1.3 79.1 + - - +
701A TYR* 1.3 68.1 + - - +
702A CYS* 3.8 1.8 - - - -
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Residues in contact with TYR 701 (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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572A GLU* 2.5 39.7 + - + -
575A PHE* 3.5 39.6 - + + +
576A CYS* 3.7 32.5 - - - -
577A GLY 4.4 5.2 - - - +
583A MET* 5.5 2.7 - - + -
688A PHE* 3.1 31.6 - + + -
689A LEU 3.7 8.5 - - - -
690A LYS* 4.6 14.8 - - + +
699A LEU 4.2 0.8 - - - -
700A ASN* 1.3 77.0 - - - +
702A CYS* 1.3 65.7 - - - +
703A GLY* 3.3 34.9 - - - -
723A ARG 5.4 0.5 - - - +
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Residues in contact with CYS 702 (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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689A LEU* 2.8 32.9 + - + +
691A MET* 3.8 29.8 - - - -
700A ASN* 3.8 2.0 - - - -
701A TYR* 1.3 80.2 - - - +
703A GLY* 1.3 59.4 + - - +
723A ARG* 2.7 47.3 + - + -
724A ALA* 3.8 26.0 - - - -
768A PHE* 3.9 6.7 - - + -
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Residues in contact with GLY 703 (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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572A GLU* 3.6 4.3 - - - -
688A PHE* 3.5 2.9 - - - -
689A LEU* 3.0 23.4 + - - -
701A TYR* 3.3 36.9 + - - -
702A CYS* 1.3 79.9 - - - +
704A HIS* 1.3 62.2 + - - +
723A ARG* 3.6 6.3 - - - -
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Residues in contact with HIS 704 (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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572A GLU* 2.7 38.0 + - - -
661A PHE* 4.6 3.3 - + - -
663A GLU* 3.1 36.4 + - + -
664A THR 5.5 2.0 - - - -
686A MET* 3.7 24.0 - - + -
687A LEU 3.2 14.8 - - - +
688A PHE* 3.6 20.6 - + + +
689A LEU* 4.6 1.3 - - - +
703A GLY* 1.3 75.3 - - - +
705A ILE* 1.3 69.9 + - - +
706A TYR* 4.2 7.2 - + - -
723A ARG* 2.8 23.5 + - - +
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Residues in contact with ILE 705 (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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685A VAL 3.7 0.2 - - - +
686A MET* 3.4 7.1 - - - +
687A LEU* 2.9 47.4 + - + +
689A LEU* 3.9 25.6 - - + -
704A HIS* 1.3 82.9 - - - +
706A TYR* 1.3 70.0 + - - +
707A THR* 4.6 9.6 - - + -
716A LEU* 4.3 34.5 - - + -
719A VAL* 3.9 22.9 - - + -
723A ARG* 3.6 17.7 - - - +
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Residues in contact with TYR 706 (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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621A ARG* 3.1 36.1 + - - -
623A TRP* 3.4 16.7 - + - -
663A GLU* 2.6 42.2 + - - -
676A LEU* 4.4 0.3 - - - +
677A PRO* 3.6 33.4 - - + -
678A LYS 4.1 5.2 - - - +
679A PHE* 3.8 27.4 - + + -
684A ASP* 5.6 3.4 - - + -
685A VAL 3.6 3.1 - - - -
686A MET* 3.9 14.1 - - + -
704A HIS* 4.2 4.2 - + - -
705A ILE* 1.3 83.2 - - - +
707A THR* 1.3 61.9 + - - +
708A PRO* 4.7 1.0 - - - +
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Residues in contact with THR 707 (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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684A ASP* 3.3 5.8 - - - +
685A VAL* 2.8 46.5 + - + +
687A LEU* 4.5 8.1 - - + -
705A ILE* 4.6 11.7 - - + -
706A TYR* 1.3 77.3 - - - +
708A PRO* 1.3 84.4 + - - +
711A CYS* 3.3 17.0 - - - +
716A LEU* 4.4 10.0 - - + +
753A LEU* 3.5 27.0 - - + +
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Residues in contact with PRO 708 (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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683A HIS* 3.3 4.5 - - + +
684A ASP* 3.1 21.5 - - - +
706A TYR 4.7 0.9 - - - +
707A THR* 1.3 105.0 + - - +
709A ILE* 1.3 61.7 + - - +
710A SER* 3.1 17.9 - - - +
711A CYS* 3.2 20.6 + - + +
753A LEU* 4.2 1.9 - - - +
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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