Contacts of the strand formed by residues 5131 - 5135 (chain o) in PDB entry 3A0B
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 PRO5131 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5064a ARG* 3.1 30.1 + - + +
5336c GLY 3.8 12.8 - - - +
5337c LEU* 3.3 58.1 - - + +
5101o THR* 4.4 1.2 + - - +
5129o PHE* 4.2 1.1 - - + -
5130o GLN* 1.3 87.3 - - - +
5132o VAL* 1.3 65.9 + - - +
5144o LEU 3.6 7.6 - - - +
5145o LEU* 4.2 5.1 - - + -
5177o TYR* 4.0 21.8 - - + +
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Residues in contact with VAL5132 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5064a ARG* 4.3 0.4 - - - +
5076o PHE* 3.8 20.9 - - + -
5096o LEU* 5.2 3.4 - - + -
5098o THR* 3.4 14.4 - - + +
5101o THR* 4.0 14.4 - - - +
5102o THR* 4.0 29.2 - - - +
5130o GLN 3.4 13.5 - - - +
5131o PRO* 1.3 84.8 - - - +
5133o THR* 1.3 63.8 + - - +
5144o LEU* 2.8 56.0 + - + +
5146o PHE* 4.3 6.3 - - + -
5177o TYR* 4.4 2.1 + - - -
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Residues in contact with THR5133 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5064a ARG* 4.1 2.9 - - - -
5107a TYR* 3.6 27.1 + - + +
5096o LEU* 4.2 4.3 - - - +
5097o VAL* 2.9 32.2 + - + +
5098o THR* 2.8 15.2 + - - -
5132o VAL* 1.3 74.5 - - - +
5134o VAL* 1.3 77.9 + - - +
5141o ARG* 4.5 7.9 - - + -
5142o ILE 2.9 32.3 - - - +
5143o PRO* 3.3 12.1 - - + -
5177o TYR* 3.7 11.6 + - - -
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Residues in contact with VAL5134 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5076o PHE* 4.1 29.6 - - + -
5078o VAL* 4.5 3.1 - - + -
5094o THR* 3.0 42.8 - - + +
5095o LYS 3.4 14.4 - - - +
5096o LEU* 4.6 4.0 - - + +
5097o VAL* 3.6 5.2 - - - -
5133o THR* 1.3 83.5 - - - +
5135o GLN* 1.3 59.8 + - - +
5141o ARG* 3.6 3.7 - - - -
5142o ILE* 2.6 59.2 + - + +
5144o LEU* 5.4 2.7 - - + -
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Residues in contact with GLN5135 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B SER 5.5 1.6 + - - -
5056a PRO* 6.0 1.4 - - - +
5103a ASP* 2.7 49.5 + - + +
5106a LEU* 5.6 3.8 - - - +
5094o THR* 4.1 4.2 - - - -
5095o LYS* 3.3 31.6 + - + +
5097o VAL* 4.4 6.4 - - + +
5134o VAL* 1.3 74.7 - - - +
5136o MET* 1.3 71.8 + - - +
5138o GLY 4.9 5.4 + - - +
5139o GLY* 3.9 12.6 + - - +
5140o GLU 3.3 15.5 - - - +
5141o ARG* 3.0 30.1 + - - -
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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