Contacts of the helix formed by residues 2166 - 2176 (chain A) in PDB entry 3ZBF
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 SER2166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2126A ARG* 4.0 2.9 - - - +
2164A ALA 4.3 0.8 + - - -
2165A HIS* 1.3 74.5 - - - +
2167A ASN* 1.3 66.1 + - - +
2168A LEU* 3.8 8.1 + - - +
2169A ASP* 2.9 31.9 + - - +
2170A VAL* 3.0 11.3 + - - +
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Residues in contact with ASN2167 (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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2123A LEU* 3.8 38.6 - - + +
2125A VAL* 4.1 12.9 - - + +
2126A ARG* 3.3 24.2 + - - +
2160A GLN* 5.5 0.2 + - - -
2166A SER* 1.3 73.4 - - - +
2168A LEU* 1.3 65.9 + - + +
2170A VAL* 3.2 21.9 + - - +
2171A LEU* 4.3 1.4 + - - +
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Residues in contact with LEU2168 (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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2166A SER* 3.2 8.6 + - - +
2167A ASN* 1.3 80.4 - - + +
2169A ASP* 1.3 62.5 + - - +
2170A VAL 3.4 0.3 + - - -
2171A LEU* 3.9 9.2 + - - +
2172A ASN* 3.9 11.5 + - - +
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Residues in contact with ASP2169 (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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2164A ALA 4.9 1.2 - - - +
2165A HIS* 3.1 28.2 - - + +
2166A SER* 2.9 26.2 + - - +
2168A LEU* 1.3 78.5 - - - +
2170A VAL* 1.3 65.4 + - - +
2171A LEU 3.4 0.2 - - - -
2172A ASN* 3.0 31.8 + - - +
2173A TYR* 2.9 19.5 + - - +
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Residues in contact with VAL2170 (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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2125A VAL* 4.3 25.6 - - + +
2126A ARG* 4.0 21.5 - - + +
2133A LEU* 5.4 2.5 - - + -
2162A TYR* 4.3 21.3 - - + -
2165A HIS* 3.9 21.5 - - + +
2166A SER 3.0 21.9 + - - +
2167A ASN* 3.2 14.6 + - - +
2169A ASP* 1.3 76.5 - - - +
2171A LEU* 1.3 60.3 + - - +
2173A TYR* 2.9 6.8 + - - +
2174A VAL* 2.9 36.4 + - + +
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Residues in contact with LEU2171 (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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2125A VAL* 6.1 0.4 - - + +
2130A PRO* 5.2 7.4 - - + -
2133A LEU* 3.8 39.9 - - + +
2134A MET* 3.8 29.4 - - + -
2167A ASN 4.3 1.6 + - - +
2168A LEU 3.9 7.1 + - - +
2169A ASP 3.4 0.6 - - - -
2170A VAL* 1.3 77.9 - - - +
2172A ASN* 1.3 67.1 + - - +
2174A VAL* 4.6 10.5 - - + +
2175A GLN* 2.8 44.1 + - - +
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Residues in contact with ASN2172 (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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2168A LEU 3.9 6.2 + - - -
2169A ASP* 3.0 37.5 + - - +
2171A LEU* 1.3 79.2 - - - +
2173A TYR* 1.3 62.1 + - - +
2175A GLN* 2.9 22.7 - - - +
2176A THR* 2.9 12.5 + - - -
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Residues in contact with TYR2173 (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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2162A TYR* 3.6 27.1 - + - -
2165A HIS* 3.5 44.2 - + + -
2169A ASP* 2.9 6.3 + - - +
2170A VAL* 2.9 9.2 + - - +
2172A ASN* 1.3 73.2 - - - +
2174A VAL* 1.3 69.8 + - - +
2176A THR* 3.0 23.0 + - + -
2178A GLY* 3.0 28.8 + - - -
2179A ARG* 2.6 50.9 + - - -
2181A GLU* 3.6 10.5 + - - -
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Residues in contact with VAL2174 (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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2128A MET 5.8 2.9 - - - +
2130A PRO* 4.1 26.5 - - + -
2133A LEU* 6.1 3.6 - - + -
2145A TRP* 4.2 15.3 - - + -
2162A TYR* 4.0 28.5 - - + +
2170A VAL* 2.9 25.3 + - + +
2171A LEU* 4.0 9.4 - - + +
2173A TYR* 1.3 74.9 - - - +
2175A GLN* 1.3 54.7 + - - +
2177A GLY* 2.6 30.0 + - - -
2178A GLY 3.5 12.1 - - - +
2179A ARG* 4.0 16.9 + - - +
2200A GLN* 4.2 3.4 - - - +
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Residues in contact with GLN2175 (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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2134A MET* 4.7 23.2 - - - +
2171A LEU* 2.8 33.8 + - - +
2172A ASN* 2.9 18.2 - - - +
2174A VAL* 1.3 73.1 - - - +
2176A THR* 1.3 52.9 + - - +
2177A GLY* 2.6 16.4 + - - -
2200A GLN* 5.1 4.9 - - - +
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Residues in contact with THR2176 (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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2172A ASN 2.9 12.7 + - - -
2173A TYR* 3.0 24.5 + - + -
2175A GLN* 1.3 73.7 - - - +
2177A GLY* 1.3 55.2 + - - +
2178A GLY* 3.1 7.2 - - - +
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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