Contacts of the helix formed by residues 6154 - 6162 (chain F) 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 GLY6154 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6122F TYR* 3.5 29.2 - - - -
6152F TYR 3.6 3.2 + - - -
6153F ASP* 1.3 72.4 + - - +
6155F LEU* 1.3 62.9 + - - +
6156F ALA 3.4 1.1 - - - -
6157F LEU* 3.5 3.9 + - - -
6158F ALA* 3.0 27.7 + - - +
6165F VAL* 3.9 19.3 - - - +
6476F PHE* 4.5 8.5 - - - -
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Residues in contact with LEU6155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6038F VAL* 3.8 28.9 - - + +
6039F SER 4.9 0.9 - - - +
6040F LEU* 4.0 36.3 - - + -
6047F VAL* 3.4 32.5 - - + -
6049F ILE* 4.3 8.7 - - + -
6122F TYR* 3.6 7.9 - - + -
6153F ASP* 2.8 23.4 + - - +
6154F GLY* 1.3 76.9 - - - +
6156F ALA* 1.3 62.9 + - - +
6158F ALA* 3.8 3.5 - - - +
6159F ALA* 3.1 19.6 + - - +
6481F LEU* 4.2 11.2 - - + -
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Residues in contact with ALA6156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6040F LEU* 3.8 18.1 - - + +
6153F ASP 4.6 0.4 + - - -
6154F GLY 3.4 0.2 - - - -
6155F LEU* 1.3 76.4 - - - +
6157F LEU* 1.3 60.8 + - - +
6160F HIS* 2.9 43.0 + - + +
6476F PHE 3.9 9.9 - - - +
6477F GLY* 3.7 28.7 - - - +
6480F PHE* 4.5 3.6 - - + -
6481F LEU* 4.2 14.7 - - + +
6497F MET* 4.3 1.6 - - - -
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Residues in contact with LEU6157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6136F MET* 4.3 14.8 - - + -
6154F GLY* 3.5 10.3 + - - +
6155F LEU 3.4 0.2 - - - -
6156F ALA* 1.3 77.0 - - - +
6158F ALA* 1.3 64.6 + - - +
6161F GLU* 3.1 29.3 + - + +
6163F VAL* 4.0 7.9 - - + +
6165F VAL* 3.9 21.3 - - + -
6218F PHE* 4.2 26.9 - - + -
6475F VAL* 3.9 25.6 - - + +
6476F PHE* 4.6 14.3 + - + -
6497F MET* 3.9 36.9 - - + +
6500F TRP* 5.5 3.1 - - + -
6501F ALA* 5.3 0.2 - - + -
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Residues in contact with ALA6158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6047F VAL* 4.6 4.7 - - + -
6122F TYR* 3.8 22.0 - - + +
6124F PRO* 3.5 15.0 - - + +
6154F GLY 3.0 18.2 + - - +
6155F LEU 3.8 3.6 - - - +
6157F LEU* 1.3 76.2 - - - +
6159F ALA* 1.3 57.7 + - - +
6162F ASN* 2.8 32.6 + - - -
6163F VAL* 3.3 23.4 + - - +
6165F VAL* 3.8 4.4 - - + +
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Residues in contact with ALA6159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6040F LEU* 3.9 21.5 - - + -
6043F PHE* 3.2 32.9 - - + -
6045F GLN 5.9 0.4 - - - +
6047F VAL* 4.0 15.4 - - + +
6124F PRO* 4.3 9.4 - - - +
6155F LEU 3.1 16.1 + - - +
6158F ALA* 1.3 82.4 - - - +
6160F HIS* 1.3 62.2 + - - +
6161F GLU 3.5 0.3 + - - -
6162F ASN* 3.8 10.2 + - - -
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Residues in contact with HIS6160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6040F LEU* 3.9 13.2 - - + +
6041F GLU 5.4 0.6 + - - -
6043F PHE* 3.3 39.8 - + - -
6156F ALA* 2.9 32.8 + - + +
6157F LEU 4.3 0.7 - - - +
6159F ALA* 1.3 74.5 - - - +
6161F GLU* 1.3 75.4 + - + +
6480F PHE* 3.7 39.5 - + - -
6494F LYS* 4.8 11.2 - - - +
6497F MET* 3.9 25.1 - - + +
6498F LYS* 5.0 1.2 + - - -
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Residues in contact with GLU6161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6157F LEU* 3.1 16.2 + - + +
6160F HIS* 1.3 88.7 - - - +
6162F ASN* 1.3 69.5 + - - +
6163F VAL* 3.4 5.3 - - + +
6494F LYS 4.6 1.7 - - - +
6497F MET* 3.4 23.9 - - + +
6498F LYS* 3.0 44.0 + - - +
6501F ALA* 3.3 24.0 - - + +
6505F ARG* 2.7 51.8 + - - -
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Residues in contact with ASN6162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6124F PRO* 3.9 21.6 + - - +
6125F ALA* 5.4 0.5 - - - -
6133F LEU* 3.0 47.5 - - + +
6134F PRO* 3.9 5.5 - - - +
6158F ALA 2.8 15.2 + - - -
6159F ALA 3.8 7.6 + - - +
6160F HIS 3.7 1.6 - - - -
6161F GLU* 1.3 81.4 - - - +
6163F VAL* 1.3 60.3 + - - +
6505F ARG* 4.5 2.7 + - - +
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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