Contacts of the strand formed by residues 655 - 661 (chain A) in PDB entry 5C58
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 ILE 655 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A ARG* 2.7 25.6 + - - -
589A ARG* 3.6 12.3 - - - +
591A PRO* 4.1 21.1 - - + -
595A GLU* 3.5 35.8 - - - +
614A LEU* 3.9 19.7 - - + -
615A GLN 3.9 15.0 - - - +
616A PRO* 5.1 0.4 - - + -
617A GLU* 2.6 19.7 + - + +
653A ASN 3.5 2.9 - - - +
654A TYR* 1.3 73.2 - - - +
656A ASN* 1.3 67.4 + - - +
676A TYR* 4.0 13.2 - - + -
677A VAL 3.5 8.3 - - - +
678A ASN* 3.4 19.7 - - - +
759A ALA* 6.0 0.2 - - - +
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Residues in contact with ASN 656 (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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654A TYR* 3.7 4.9 + - + +
655A ILE* 1.3 76.5 - - - +
657A LEU* 1.3 89.0 + - - +
658A ALA 3.4 1.4 + - - -
676A TYR* 3.5 11.8 - - - -
677A VAL* 3.0 33.3 + - - +
714A PHE* 3.5 28.3 - - + -
759A ALA* 3.8 38.3 + - - +
760A ALA* 4.3 10.5 - - - +
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Residues in contact with LEU 657 (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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608A GLN* 3.5 30.5 - - + +
656A ASN* 1.3 89.5 + - - +
658A ALA* 1.3 61.3 + - - +
659A ILE* 4.2 11.7 - - + +
674A ALA* 3.7 26.9 - - + -
675A ALA* 3.6 8.5 - - - +
676A TYR* 3.4 44.2 - - + +
714A PHE* 5.7 0.2 - - - -
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Residues in contact with ALA 658 (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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656A ASN 3.4 0.8 + - - -
657A LEU* 1.3 73.7 - - - +
659A ILE* 1.3 62.5 + - - +
661A ARG* 3.5 35.5 - - - +
674A ALA* 3.2 4.9 - - - +
675A ALA 2.9 30.9 + - - +
677A VAL* 3.8 19.5 - - + -
714A PHE* 4.3 10.5 - - + -
716A SER* 4.2 1.8 - - - +
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Residues in contact with ILE 659 (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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606A SER* 6.1 4.0 - - - -
657A LEU* 4.2 9.4 - - + +
658A ALA* 1.3 76.4 - - - +
660A ASP* 1.3 67.9 + - + +
661A ARG* 3.0 32.5 + - - +
671A ILE* 6.3 1.3 - - + -
672A GLY* 5.1 6.7 - - - +
673A ASN 3.7 5.8 - - - +
674A ALA* 4.0 16.2 - - + -
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Residues in contact with ASP 660 (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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659A ILE* 1.3 82.6 - - + +
661A ARG* 1.3 67.4 + - - +
671A ILE* 3.1 46.4 - - + +
672A GLY 4.6 7.1 - - - +
673A ASN 3.5 4.8 + - - -
718A LYS* 2.6 48.5 + - - +
749A THR* 5.6 4.0 - - - +
49B SER* 5.9 1.3 - - - -
102B ASP* 4.7 7.3 - - - +
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Residues in contact with ARG 661 (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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658A ALA* 3.5 34.7 - - + +
659A ILE 3.0 29.2 + - - +
660A ASP* 1.3 97.6 + - - +
662A ASN* 1.3 62.1 + - - +
670A SER 4.1 6.6 - - - +
673A ASN* 3.1 31.6 + - - +
674A ALA* 5.0 0.2 - - - -
675A ALA* 4.6 7.2 - - + +
677A VAL* 4.6 10.3 - - - +
714A PHE* 5.6 1.0 - - - -
716A SER* 2.6 30.8 + - - -
718A LYS* 3.3 41.6 + - - +
720A TRP* 3.5 24.5 - - + -
749A THR* 3.4 16.3 + - - +
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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