Contacts of the strand formed by residues 958 - 965 (chain A) in PDB entry 5J9H
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 958 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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688A SER* 2.9 51.9 + - - -
689A LEU 3.2 8.7 - - - +
690A PRO* 3.4 30.4 - - + +
846A THR* 3.5 25.2 + - - +
955A SER 4.3 9.7 + - - +
956A SER* 3.7 7.9 + - - +
957A LEU* 1.3 77.8 - - - +
959A ASP* 1.3 67.5 + - - +
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Residues in contact with ASP 959 (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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688A SER* 3.3 6.3 - - - -
689A LEU 2.9 28.8 + - - +
691A SER* 3.2 11.2 + - - -
720A GLN* 3.1 25.6 + - - -
813A ARG* 2.8 36.3 + - - +
830A SER* 5.7 1.8 - - - +
843A LEU* 5.7 5.4 - - + -
844A ILE 3.4 15.3 - - - +
845A GLY* 4.4 10.2 - - - -
846A THR* 4.6 5.2 + - - +
958A ARG* 1.3 75.4 - - - +
960A HIS* 1.3 63.1 - - - +
961A ILE* 4.0 10.3 - - + +
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Residues in contact with HIS 960 (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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686A ASP* 2.8 41.1 + - - -
687A PHE* 3.5 19.6 + - - -
688A SER* 4.6 5.3 + - - +
842A CYS 3.6 1.0 - - - +
843A LEU* 3.5 4.9 - - - +
844A ILE* 2.8 64.8 + - + +
959A ASP* 1.3 74.4 - - - +
961A ILE* 1.3 69.9 + - - +
962A ASN* 4.3 4.9 - - + -
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Residues in contact with ILE 961 (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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686A ASP* 3.5 3.3 - - - -
687A PHE* 3.0 63.4 + - + +
689A LEU* 3.7 35.2 - - + +
717A LEU* 4.2 16.4 - - + -
813A ARG* 4.7 5.6 - - - +
841A VAL* 4.4 7.9 - - + -
842A CYS 3.5 5.8 - - - +
843A LEU* 3.8 20.0 - - + -
959A ASP* 4.0 15.9 - - + +
960A HIS* 1.3 85.5 - - - +
962A ASN* 1.3 64.7 + - - +
963A VAL* 4.1 17.0 - - + -
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Residues in contact with ASN 962 (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 GLU* 3.2 23.9 + - - +
685A LEU 3.4 7.8 + - - -
686A ASP* 3.1 22.4 + - - +
840A LYS* 3.5 20.2 + - - +
841A VAL* 3.4 5.2 - - - +
842A CYS* 3.0 42.5 + - + +
844A ILE* 6.4 1.3 - - + -
960A HIS* 4.3 5.8 - - + -
961A ILE* 1.3 73.6 - - - +
963A VAL* 1.3 73.7 + - - +
964A ILE* 4.1 4.7 - - - +
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Residues in contact with VAL 963 (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 LEU* 6.0 0.7 - - + -
684A GLU* 3.2 8.7 - - - +
685A LEU* 2.7 51.7 + - + +
713A PHE* 3.9 28.7 - - + -
715A LEU* 3.8 26.7 - - + -
839A VAL* 4.1 11.9 - - + -
840A LYS 3.4 9.4 - - - +
841A VAL* 4.2 12.8 - - + -
961A ILE* 4.1 12.6 - - + -
962A ASN* 1.3 79.6 - - - +
964A ILE* 1.3 66.5 + - - +
965A VAL* 4.7 2.2 - - + -
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Residues in contact with ILE 964 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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674A SER* 4.7 3.1 - - - +
676A ILE* 4.9 15.3 - - + -
681A THR* 4.2 27.6 - - + +
683A LEU 3.4 11.7 - - - +
684A GLU* 3.4 36.6 - - + +
838A SER 3.9 0.2 - - - +
839A VAL* 3.4 5.4 - - - +
840A LYS* 3.1 66.0 + - + +
962A ASN* 4.1 4.5 - - - +
963A VAL* 1.3 75.2 - - - +
965A VAL* 1.3 64.9 + - - +
966A SER 4.2 0.2 + - - -
971A PHE* 4.6 1.9 - - + -
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Residues in contact with VAL 965 (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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681A THR* 3.5 6.1 - - - -
682A ASP* 2.8 40.8 + - + +
683A LEU* 2.9 35.9 + - + +
701A LEU* 4.2 3.4 - - + -
713A PHE* 3.8 34.5 - - + -
819A LEU* 3.7 34.5 - - + -
838A SER 3.4 4.7 - - - +
839A VAL* 4.3 4.0 - - + -
963A VAL* 4.7 2.5 - - + -
964A ILE* 1.3 76.7 - - - +
966A SER* 1.3 66.1 + - - +
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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