Contacts of the strand formed by residues 2166 - 2171 (chain A) in PDB entry 5MV9
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 TYR2166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2161A SER* 4.4 5.9 - - - -
2162A SER* 3.4 16.9 + - - -
2163A GLY* 3.0 42.7 + - - +
2164A ASN 3.7 0.2 - - - -
2165A THR* 1.3 83.3 - - - +
2167A PHE* 1.3 68.1 + - - +
2168A HIS* 4.4 0.9 - - + -
2181A LEU* 4.1 17.0 - - + -
2182A CYS 3.2 13.0 - - - +
2183A GLU* 5.0 1.8 - - + -
2184A THR* 3.2 8.5 + - - -
2187A GLY* 3.9 2.9 - - - -
469B GLU* 3.2 33.3 - - + +
470B GLY 4.7 5.3 + - - -
474B SER* 4.7 5.0 - - - -
475B PRO* 4.1 31.4 - - + +
476B ILE* 3.5 38.4 - - + -
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Residues in contact with PHE2167 (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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2133A ILE* 5.1 3.8 - - + -
2138A VAL* 5.7 5.6 - - + -
2160A TRP* 4.5 4.0 - + - -
2161A SER 3.2 19.7 - - - -
2162A SER* 3.9 2.0 - - - -
2166A TYR* 1.3 78.1 - - - +
2168A HIS* 1.3 60.5 + - - +
2169A ILE* 3.4 22.0 - - + -
2180A LEU* 3.7 2.8 - - + +
2181A LEU* 3.7 1.1 - - - +
2182A CYS* 2.9 40.7 + - + +
2184A THR* 3.9 6.7 - - + -
2187A GLY* 3.8 16.6 - - - -
2190A MET* 3.6 52.9 - - + -
2191A ASP* 3.5 23.8 - - + -
2194A LEU* 3.6 27.4 - - + -
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Residues in contact with HIS2168 (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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2121A THR* 5.5 1.2 - - - +
2160A TRP* 3.2 5.9 - - - +
2161A SER* 2.9 49.8 + - - +
2166A TYR* 4.4 2.0 - - + -
2167A PHE* 1.3 74.9 - - - +
2169A ILE* 1.3 89.5 + - - +
2170A THR* 3.6 16.2 + - - -
2179A LYS* 3.5 28.3 - - + +
2180A LEU 3.3 16.3 + - - -
2181A LEU* 3.6 19.9 + - + -
475B PRO* 3.6 34.8 + - + +
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Residues in contact with ILE2169 (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 VAL* 4.1 22.0 - - + -
2152A HIS* 4.3 6.7 - - + -
2157A ILE* 4.1 26.7 - - + -
2159A ASN 3.5 7.4 - - - +
2160A TRP* 3.9 0.4 - - + -
2167A PHE* 3.4 32.1 - - + -
2168A HIS* 1.3 82.1 + - - +
2170A THR* 1.3 60.4 + - - +
2171A ILE* 3.8 25.1 - - + +
2179A LYS* 3.5 2.1 - - - -
2180A LEU* 2.8 54.4 + - + -
2194A LEU* 3.7 16.2 - - + -
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Residues in contact with THR2170 (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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2157A ILE* 3.6 5.7 - - - +
2158A SER* 3.0 40.1 + - - +
2159A ASN* 2.8 32.9 + - + +
2168A HIS* 3.6 17.8 + - - -
2169A ILE* 1.3 71.4 - - - +
2171A ILE* 1.3 62.5 + - - +
2172A GLY 4.2 6.7 - - - +
2178A SER 3.8 8.5 - - - +
2179A LYS* 4.2 10.5 - - + +
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Residues in contact with ILE2171 (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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2152A HIS* 3.7 55.2 - - + +
2156A LYS* 3.4 26.0 - - + +
2157A ILE* 4.6 2.5 - - + -
2169A ILE* 3.8 30.1 - - + +
2170A THR* 1.3 75.5 - - - +
2172A GLY* 1.3 63.1 - - - +
2173A ASN 3.9 1.2 + - - -
2178A SER* 2.7 55.6 + - - +
2180A LEU* 4.4 8.1 - - + -
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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