Contacts of the strand formed by residues 683 - 690 (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 LEU 683 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681A THR* 3.7 1.5 - - - -
682A ASP* 1.3 80.4 - - - +
684A GLU* 1.3 71.5 + - - +
685A LEU* 4.5 10.8 - - + -
697A TYR* 4.0 17.0 - - + +
699A ARG* 3.9 21.3 - - - +
701A LEU* 3.7 35.4 - - + -
713A PHE* 3.6 37.5 - - + -
963A VAL* 5.2 1.1 - - + -
964A ILE* 3.4 10.1 - - - +
965A VAL* 2.9 35.5 + - + +
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Residues in contact with GLU 684 (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* 1.3 78.6 - - - +
685A LEU* 1.3 74.7 + - - +
686A ASP* 4.3 6.0 + - + +
962A ASN* 3.2 19.7 + - - +
963A VAL 3.2 11.0 - - - +
964A ILE* 3.4 24.7 - - + +
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Residues in contact with LEU 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A LEU* 4.3 13.4 - - + +
684A GLU* 1.3 78.3 - - - +
686A ASP* 1.3 65.5 + - - +
687A PHE* 4.1 15.9 - - + -
695A TYR* 4.8 3.1 - - + +
697A TYR* 3.8 56.5 - - + +
713A PHE* 4.4 3.6 - - + -
715A LEU* 3.9 24.9 - - + -
962A ASN* 3.4 3.6 + - - -
963A VAL* 2.7 48.0 + - + +
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Residues in contact with ASP 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A GLU* 4.3 9.1 + - + +
685A LEU* 1.3 76.5 - - - +
687A PHE* 1.3 65.8 + - - +
960A HIS* 2.8 36.5 + - - -
961A ILE 3.5 5.4 - - - +
962A ASN* 3.1 23.4 + - - +
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Residues in contact with PHE 687 (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 LEU* 4.1 20.9 - - + -
686A ASP* 1.3 88.8 + - - +
688A SER* 1.3 72.7 + - - +
689A LEU* 4.1 24.7 - - + -
695A TYR* 3.8 36.3 - + - -
715A LEU* 4.9 1.3 - - + -
717A LEU* 4.0 6.3 - - + -
960A HIS* 3.5 12.1 + - - -
961A ILE* 3.0 65.0 + - + +
963A VAL* 5.0 0.9 - - + -
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Residues in contact with SER 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A PHE* 1.3 83.6 - - - +
689A LEU* 1.3 62.7 + - - +
958A ARG* 2.9 40.0 + - - -
959A ASP 3.3 11.9 - - - -
960A HIS* 4.6 6.5 - - - +
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Residues in contact with LEU 689 (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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687A PHE* 4.1 11.9 - - + -
688A SER* 1.3 78.1 - - - +
690A PRO* 1.4 81.0 - - + +
693A ALA* 3.5 28.0 - - + +
694A SER 4.5 1.8 - - - +
695A TYR* 4.0 34.5 - - + -
717A LEU* 4.2 14.1 - - + -
813A ARG* 3.6 17.9 - - - +
958A ARG* 3.2 4.4 - - - -
959A ASP* 2.9 32.2 + - - +
961A ILE* 3.7 16.6 - - + -
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Residues in contact with PRO 690 (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* 1.4 92.2 - - + +
691A SER* 1.3 64.2 + - - +
692A SER* 4.3 2.2 - - - +
693A ALA* 3.0 32.9 + - + +
813A ARG* 2.9 12.5 + - - -
955A SER* 3.7 35.0 - - - +
957A LEU 3.3 8.5 - - - +
958A ARG* 3.4 30.7 - - + +
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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