Contacts of the helix formed by residues 6426 - 6439 (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 PHE6426 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F COA 3.8 18.8 - - - -
6221F SER* 4.8 1.8 - - - -
6247F SER* 3.3 34.5 - - - -
6248F GLY* 4.0 4.9 - - - -
6252F THR* 4.3 11.0 - - + -
6255F LEU* 6.2 0.9 - - + -
6350F ILE* 4.2 9.4 - - + -
6354F GLU* 3.5 36.3 - - + -
6355F PHE* 5.2 1.1 - + - -
6359F ILE* 3.7 31.6 - - + -
6422F ALA* 2.8 16.9 + - - +
6425F MET* 1.3 102.2 - - + +
6427F GLY* 1.3 64.2 + - - +
6429F PRO* 3.5 4.9 - - - -
6430F SER* 2.8 34.2 + - - +
6468F HIS* 3.9 8.5 - + - -
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Residues in contact with GLY6427 (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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6350F ILE* 3.9 24.4 - - - +
6354F GLU* 5.5 0.4 - - - +
6422F ALA 3.2 9.4 + - - -
6423F ASP* 3.7 8.3 - - - -
6426F PHE* 1.3 81.1 - - - +
6428F VAL* 1.3 62.8 + - - +
6430F SER* 3.7 1.6 - - - -
6431F VAL* 3.3 25.1 + - - +
6540F LYS* 4.4 13.1 - - - +
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Residues in contact with VAL6428 (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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6423F ASP* 2.7 25.5 + - + +
6424F VAL* 4.9 2.0 - - - -
6427F GLY* 1.3 68.6 - - - -
6429F PRO* 1.3 69.0 - - + +
6430F SER 3.3 0.2 + - - -
6431F VAL* 3.3 2.6 + - - +
6432F ILE* 3.0 48.4 + - + +
6540F LYS* 5.4 0.2 - - + -
6543F GLU* 4.0 22.7 - - + +
6544F VAL* 4.1 22.9 - - + +
6547F TRP* 3.6 38.1 - - + -
6548F THR* 5.2 0.7 - - - +
6551F PHE* 6.4 0.4 - - + -
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Residues in contact with PRO6429 (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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6249F VAL* 3.8 8.5 - - + -
6251F LEU* 3.6 40.7 - - + +
6252F THR 4.1 0.9 - - - +
6423F ASP 3.5 2.7 - - - +
6424F VAL 3.2 26.0 - - - +
6425F MET 3.6 11.2 - - - +
6426F PHE 3.4 11.9 - - - +
6428F VAL* 1.3 96.4 - - + +
6430F SER* 1.3 55.9 + - - +
6432F ILE* 3.3 7.1 + - + +
6433F VAL* 3.0 33.8 + - - +
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Residues in contact with SER6430 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6248F GLY 4.6 5.9 + - - -
6249F VAL* 4.0 16.2 - - - +
6348F VAL* 3.7 23.6 - - - +
6349F GLY 4.4 1.7 + - - -
6350F ILE* 3.4 21.9 - - - +
6426F PHE* 2.8 25.5 + - - -
6427F GLY 3.7 3.4 - - - -
6428F VAL 3.2 0.2 - - - -
6429F PRO* 1.3 77.4 - - - +
6431F VAL* 1.3 57.7 + - - +
6433F VAL* 3.3 2.8 + - - +
6434F ALA* 3.0 28.9 + - - +
6446F MET* 3.7 8.0 - - - +
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Residues in contact with VAL6431 (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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6350F ILE* 6.0 0.4 - - + -
6427F GLY 3.3 15.0 + - - +
6428F VAL 3.3 3.8 + - - +
6430F SER* 1.3 76.2 - - - +
6432F ILE* 1.3 59.1 + - - +
6434F ALA* 3.3 0.9 + - - +
6435F ARG* 2.9 61.3 + - - +
6446F MET* 3.8 24.2 - - + -
6520F TYR* 3.5 11.2 - - - +
6539F LEU* 3.4 30.3 - - + +
6540F LYS* 4.0 9.0 - - + -
6544F VAL* 3.9 13.2 - - + -
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Residues in contact with ILE6432 (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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6251F LEU* 3.5 24.2 - - + -
6336F GLN* 4.5 0.7 - - - +
6428F VAL* 3.0 41.1 + - + +
6429F PRO* 3.7 5.2 - - + +
6431F VAL* 1.3 77.2 - - - +
6433F VAL* 1.3 58.4 + - - +
6435F ARG* 3.6 7.1 + - - +
6436F ASN* 2.7 47.2 + - - +
6544F VAL* 4.0 21.5 - - + -
6548F THR* 4.5 8.7 - - + +
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Residues in contact with VAL6433 (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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6228F SER* 4.6 8.3 - - - +
6249F VAL* 3.8 27.4 - - + -
6250F ALA* 5.5 1.1 - - + -
6251F LEU* 3.8 13.9 - - + +
6336F GLN* 3.5 23.7 + - - +
6346F TYR* 3.8 33.0 - - + +
6348F VAL* 4.5 3.1 - - + -
6429F PRO 3.0 20.5 + - - +
6430F SER 3.6 4.3 - - - +
6432F ILE* 1.3 74.6 - - - +
6434F ALA* 1.3 59.6 + - - +
6436F ASN* 3.4 2.6 + - - +
6437F HIS* 3.0 27.9 + - + +
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Residues in contact with ALA6434 (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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6348F VAL* 4.4 7.0 - - + -
6430F SER 3.0 12.3 + - - +
6431F VAL 3.7 2.0 - - - +
6433F VAL* 1.3 79.8 - - - +
6435F ARG* 1.3 57.4 + - - +
6437F HIS* 3.3 4.4 + - - +
6438F ARG* 2.9 30.5 + - - +
6444F THR* 3.7 16.5 - - + +
6446F MET* 3.5 41.1 - - + -
6520F TYR* 3.9 7.9 - - + -
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Residues in contact with ARG6435 (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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6431F VAL* 2.9 38.0 + - - +
6432F ILE* 3.9 7.2 - - - +
6434F ALA* 1.3 75.4 - - - +
6436F ASN* 1.3 57.9 + - - +
6438F ARG* 3.5 22.4 + - - +
6439F ASP* 2.7 41.8 + - - +
6520F TYR* 3.4 17.2 + - + +
6524F GLU* 2.9 27.0 + - - +
6539F LEU 4.9 0.2 + - - -
6541F ASP* 3.0 41.8 + - - +
6544F VAL* 3.7 24.0 - - - +
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Residues in contact with ASN6436 (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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6336F GLN* 3.7 36.3 + - + +
6337F ALA* 4.7 1.9 + - - -
6339F ARG* 3.3 36.8 + - - +
6341F PHE* 3.7 4.7 - - + -
6432F ILE* 2.7 42.3 + - - +
6433F VAL 3.8 3.6 - - - +
6435F ARG* 1.3 77.9 - - - +
6437F HIS* 1.3 65.9 + - - +
6439F ASP* 3.5 3.5 + - - -
6440F ALA* 3.3 18.9 + - - +
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Residues in contact with HIS6437 (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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6231F VAL* 3.9 9.0 - - + +
6341F PHE* 3.4 23.6 - + - -
6342F HIS 3.3 26.0 - - - -
6344F VAL* 2.8 24.4 + - + -
6346F TYR* 3.3 41.4 - + + +
6433F VAL* 3.0 18.1 + - + +
6434F ALA* 3.6 6.1 - - - +
6436F ASN* 1.3 76.0 - - - +
6438F ARG* 1.3 64.2 + - - +
6440F ALA* 3.2 12.1 + - - +
6442F ALA* 3.3 35.6 + - + +
6443F PRO 3.9 1.3 - - - -
6444F THR* 3.4 14.6 - - + +
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Residues in contact with ARG6438 (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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6434F ALA 2.9 17.5 + - - +
6435F ARG* 3.5 25.8 + - - +
6437F HIS* 1.3 76.7 - - - +
6439F ASP* 1.3 86.8 + - - +
6441F GLY* 2.8 22.7 + - - -
6442F ALA 3.8 6.7 + - - +
6444F THR* 3.4 11.4 + - - +
6519F GLU* 5.4 0.9 - - - +
6520F TYR* 3.3 32.4 - - + +
6521F ASN* 3.0 32.7 + - - -
6522F GLN* 3.4 24.4 + - - +
6524F GLU* 3.4 27.1 + - - +
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Residues in contact with ASP6439 (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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6339F ARG* 3.5 31.3 + - - +
6435F ARG* 2.7 30.5 + - - +
6436F ASN* 3.5 2.5 + - - +
6438F ARG* 1.3 105.0 + - - +
6440F ALA* 1.3 57.7 + - - +
6441F GLY 3.2 1.9 + - - -
6522F GLN* 3.4 13.5 + - - +
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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