Contacts of the helix formed by residues 2156 - 2165 (chain A) in PDB entry 4ASI
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 GLU2156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2124A GLU* 4.9 4.0 - - - +
2126A ARG* 3.8 26.8 - - + +
2155A LEU* 1.3 80.0 - - + +
2157A PRO* 1.3 78.3 - - + +
2158A GLU* 3.0 26.7 + - - +
2159A GLY* 3.1 25.5 + - - +
2160A THR* 2.9 19.6 + - - -
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Residues in contact with PRO2157 (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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2126A ARG* 3.8 11.0 - - - +
2155A LEU 3.8 0.4 - - - +
2156A GLU* 1.3 90.5 - - + +
2158A GLU* 1.3 64.4 + - - +
2160A THR* 3.1 3.2 + - - -
2161A VAL* 2.8 27.4 + - - +
2221A VAL* 3.8 28.5 - - + +
2224A ALA* 3.9 11.0 - - + -
2225A ASP* 3.8 22.9 - - + +
2228A ASP* 3.3 23.5 - - - +
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Residues in contact with GLU2158 (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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2156A GLU* 3.0 19.7 + - - +
2157A PRO* 1.3 78.7 - - - +
2159A GLY* 1.3 57.5 + - - +
2161A VAL* 3.9 2.6 - - - +
2162A GLU* 3.1 25.1 + - - +
2217A HIS* 2.9 32.6 + - + +
2221A VAL* 3.4 23.2 - - - +
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Residues in contact with GLY2159 (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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2155A LEU* 3.5 21.0 - - - +
2156A GLU* 3.1 20.8 + - - -
2157A PRO 3.1 0.6 - - - -
2158A GLU* 1.3 74.6 - - - +
2160A THR* 1.3 64.6 + - - +
2162A GLU* 3.5 8.7 - - - +
2163A ILE* 3.4 21.3 + - - +
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Residues in contact with THR2160 (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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2155A LEU* 3.3 31.5 + - + +
2156A GLU 2.9 18.8 + - - -
2157A PRO* 3.1 7.6 + - - +
2159A GLY* 1.3 74.3 - - - +
2161A VAL* 1.3 61.7 + - + +
2163A ILE* 3.1 3.7 + - - +
2164A LYS* 2.7 42.2 + - + +
2224A ALA* 4.5 13.5 - - + -
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Residues in contact with VAL2161 (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 PRO 2.8 14.4 + - - +
2158A GLU 3.9 3.4 - - - +
2160A THR* 1.3 76.8 - - + +
2162A GLU* 1.3 67.2 + - - +
2165A PHE* 2.8 52.6 + - + +
2166A ARG* 4.5 0.2 - - - -
2170A LEU* 5.8 0.2 - - + -
2217A HIS* 3.7 29.4 - - + +
2220A ALA* 3.4 44.0 - - + +
2221A VAL* 3.6 12.3 - - + +
2224A ALA* 4.2 6.7 - - + -
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Residues in contact with GLU2162 (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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2158A GLU 3.1 13.3 + - - +
2159A GLY* 3.5 14.4 - - - +
2161A VAL* 1.3 80.6 - - - +
2163A ILE* 1.3 62.8 + - + +
2166A ARG* 3.4 18.1 - - - +
2217A HIS* 5.0 9.5 - - - -
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Residues in contact with ILE2163 (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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2155A LEU* 4.0 18.2 - - + -
2159A GLY 3.4 12.9 + - - +
2160A THR* 3.1 6.9 + - - +
2162A GLU* 1.3 82.2 - - + +
2164A LYS* 1.3 77.0 + - + +
2165A PHE 3.7 0.9 - - - -
2166A ARG* 2.5 39.3 + - - +
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Residues in contact with LYS2164 (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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2160A THR* 2.7 28.6 + - + +
2161A VAL* 3.8 0.4 - - - -
2163A ILE* 1.3 96.2 - - + +
2165A PHE* 1.3 65.7 + - - +
2166A ARG* 3.9 5.4 - - - +
2169A ASP* 4.5 7.8 - - - +
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Residues in contact with PHE2165 (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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2161A VAL* 2.8 45.4 + - + +
2164A LYS* 1.3 75.5 - - - +
2166A ARG* 1.3 66.6 + - - +
2169A ASP* 3.6 38.1 - - + -
2170A LEU* 3.9 19.5 - - + +
2173A THR* 3.7 18.4 - - + -
2220A ALA* 3.9 28.0 - - + -
2223A PHE* 3.7 38.4 - + + -
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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