Contacts of the helix formed by residues 2154 - 2162 (chain B) in PDB entry 2H7C
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 GLY2154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2122B TYR* 3.5 31.8 - - - -
2152B TYR 3.6 2.6 + - - -
2153B ASP* 1.3 72.6 + - - +
2155B LEU* 1.3 63.4 + - - +
2156B ALA 3.4 1.5 + - - -
2157B LEU* 3.4 3.9 + - - -
2158B ALA* 3.0 26.3 + - - +
2165B VAL* 4.0 18.1 - - - +
2476B PHE* 4.6 7.9 - - - -
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Residues in contact with LEU2155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2038B VAL* 3.9 33.9 - - + +
2039B SER 4.8 1.6 - - - +
2040B LEU* 4.1 26.5 - - + -
2047B VAL* 3.6 32.9 - - + +
2049B ILE* 4.7 4.3 - - + -
2122B TYR* 3.5 10.2 - - + -
2153B ASP* 2.9 23.7 + - - +
2154B GLY* 1.3 76.6 - - - +
2156B ALA* 1.3 64.5 + - - +
2158B ALA* 3.9 3.2 - - - +
2159B ALA* 3.1 21.0 + - - +
2481B LEU* 3.9 19.3 - - + -
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Residues in contact with ALA2156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2040B LEU* 3.7 18.2 - - + -
2153B ASP 4.7 0.6 + - - -
2154B GLY 3.4 0.4 - - - -
2155B LEU* 1.3 76.3 - - - +
2157B LEU* 1.3 62.0 + - - +
2159B ALA 3.4 0.2 + - - -
2160B HIS* 2.9 43.6 + - + +
2476B PHE 4.0 10.3 - - - +
2477B GLY* 3.8 26.7 - - - +
2480B PHE* 4.4 4.0 - - + -
2481B LEU* 4.2 15.9 - - + +
2497B MET* 4.4 1.6 - - - -
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Residues in contact with LEU2157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2136B MET* 4.3 14.8 - - + -
2154B GLY 3.4 8.7 + - - +
2156B ALA* 1.3 77.0 - - - +
2158B ALA* 1.3 63.9 + - - +
2161B GLU* 3.0 34.6 + - + +
2163B VAL* 4.1 6.9 - - + +
2165B VAL* 4.0 21.3 - - + -
2218B PHE* 4.2 25.8 - - + -
2475B VAL* 4.0 17.0 - - + +
2476B PHE* 4.7 15.9 + - + -
2497B MET* 3.8 41.8 - - + +
2500B TRP* 5.6 2.7 - - + -
2501B ALA* 5.1 0.2 - - + -
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Residues in contact with ALA2158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2047B VAL* 4.7 4.3 - - + -
2122B TYR* 3.7 22.7 - - + +
2124B PRO* 3.3 16.6 - - + +
2154B GLY 3.0 18.6 + - - +
2155B LEU 3.9 3.1 - - - +
2157B LEU* 1.3 77.3 - - - +
2159B ALA* 1.3 57.2 + - - +
2162B ASN* 2.9 30.1 + - - -
2163B VAL* 3.2 23.1 - - - +
2165B VAL* 3.8 5.9 - - + +
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Residues in contact with ALA2159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2040B LEU* 3.8 21.5 - - + -
2043B PHE* 3.2 34.4 - - + -
2045B GLN 6.0 0.2 - - - +
2047B VAL* 4.0 14.4 - - + -
2124B PRO* 4.3 9.3 - - - +
2155B LEU 3.1 16.7 + - - +
2158B ALA* 1.3 79.3 - - - +
2160B HIS* 1.3 64.3 + - - +
2161B GLU 3.5 0.3 + - - -
2162B ASN* 3.7 10.4 + - - +
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Residues in contact with HIS2160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2040B LEU* 3.9 13.9 - - + +
2041B GLU 5.3 0.6 + - - -
2043B PHE* 3.5 35.8 - + - -
2156B ALA* 2.9 35.3 + - + +
2157B LEU 4.3 0.9 - - - +
2159B ALA* 1.3 74.8 - - - +
2161B GLU* 1.3 71.4 + - + +
2162B ASN 3.6 0.2 - - - -
2480B PHE* 3.5 44.6 - + - -
2494B LYS* 4.8 9.8 - - - +
2497B MET* 3.8 25.1 - - + +
2498B LYS* 5.2 1.4 + - - -
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Residues in contact with GLU2161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2157B LEU* 3.0 18.1 + - + +
2160B HIS* 1.3 85.4 - - + +
2162B ASN* 1.3 70.5 + - - +
2163B VAL* 3.3 5.1 - - + +
2494B LYS 4.4 2.4 - - - +
2497B MET* 3.4 32.7 - - + +
2498B LYS* 3.2 47.6 + - - +
2501B ALA* 3.4 13.5 - - + -
2505B ARG* 2.8 50.1 + - - -
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Residues in contact with ASN2162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2124B PRO* 3.9 15.5 + - - +
2125B ALA* 5.6 0.3 - - - -
2133B LEU* 3.2 43.1 - - + +
2134B PRO* 4.0 4.7 - - - +
2158B ALA 2.9 15.9 + - - -
2159B ALA 3.7 7.2 + - - +
2160B HIS 3.6 1.6 - - - -
2161B GLU* 1.3 81.0 - - - +
2163B VAL* 1.3 58.4 + - - +
2505B ARG* 4.7 1.9 + - - +
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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