Contacts of the strand formed by residues 2165 - 2168 (chain A) in PDB entry 4YNP
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 PHE2165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2132A ARG* 3.6 52.4 - - + +
2133A ILE* 4.0 21.1 - - + -
2137A GLU 3.3 30.6 - - - +
2138A TRP* 3.5 33.2 - + - -
2139A VAL* 3.5 9.9 - - - +
2163A GLY 3.5 4.6 + - - -
2164A GLN* 1.3 84.3 - - - +
2166A ILE* 1.3 62.1 + - - +
2167A ILE 3.8 18.4 - - - -
2168A GLU* 3.8 7.4 - - - -
2238A GLY* 4.3 5.6 - - - -
2239A LEU 4.0 1.6 - - - -
2240A TYR* 3.7 34.5 - + + -
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Residues in contact with ILE2166 (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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2138A TRP* 3.5 3.5 - - - +
2139A VAL* 3.0 37.3 + - + +
2142A LEU* 4.1 14.0 - - + +
2160A LEU* 4.2 20.4 - - + -
2164A GLN* 3.5 14.6 - - + +
2165A PHE* 1.3 78.2 - - - +
2167A ILE* 1.3 74.6 + - + +
2224A CYS* 3.5 31.6 - - - -
2239A LEU* 2.9 19.2 + - + +
2240A TYR 4.1 2.7 - - - -
2241A ALA* 3.7 22.4 - - + +
2251A LEU* 4.0 19.5 - - + -
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Residues in contact with ILE2167 (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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2071A LYS* 6.2 0.7 - - - +
2138A TRP* 3.9 24.9 - - + -
2142A LEU* 3.7 24.7 - - + -
2165A PHE* 3.8 6.7 - - - -
2166A ILE* 1.3 94.9 - - + +
2168A GLU* 1.3 72.4 + - - +
2211A ASN* 3.5 19.5 - - + +
2212A GLU* 4.5 7.0 - - + +
2213A ALA* 3.8 28.5 - - + +
2216A ILE* 4.6 2.9 - - + -
2238A GLY* 3.7 0.3 - - - -
2239A LEU* 2.8 45.0 + - + +
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Residues in contact with GLU2168 (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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2075A ASN* 4.0 3.6 + - - -
2133A ILE* 3.4 21.6 - - + +
2136A HIS* 4.2 9.0 - - - -
2138A TRP* 3.5 21.2 + - + +
2165A PHE* 3.8 6.7 - - + -
2167A ILE* 1.3 79.5 - - - +
2169A TYR* 1.3 56.6 + - - +
2170A LEU* 3.5 26.5 - - + +
2211A ASN* 2.5 33.6 + - - -
2213A ALA* 3.9 1.6 - - - +
2236A ARG* 2.9 51.0 + - + +
2237A ILE 3.3 17.9 - - - +
2238A GLY* 4.2 2.2 - - - -
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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