Contacts of the helix formed by residues 6374 - 6385 (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 ASP6374 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1461A PRO* 4.0 4.9 - - - +
1462A LYS* 3.5 48.8 + - + +
1463A THR* 6.1 0.9 - - - +
6373F LEU* 1.3 77.7 - - - +
6375F GLN* 1.3 66.4 + - - +
6376F LYS* 3.6 4.7 + - + +
6377F THR* 2.7 43.4 + - - -
6378F ALA* 3.0 20.3 + - - +
6404F LEU* 5.1 0.4 - - - -
6410F THR* 3.5 10.7 - - + +
6413F LYS* 4.8 3.8 - - - +
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Residues in contact with GLN6375 (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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6374F ASP* 1.3 73.9 - - - +
6376F LYS* 1.3 63.8 + - + +
6378F ALA* 3.2 6.3 + - - +
6379F MET* 3.0 37.9 + - + +
6397F PRO 5.4 0.2 - - - +
6400F THR* 4.1 8.8 - - + +
6401F GLU* 3.8 20.9 + - - +
6404F LEU* 3.8 25.1 - - + -
6405F GLY* 3.3 31.5 - - - +
6413F LYS* 3.2 30.1 - - - +
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Residues in contact with LYS6376 (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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1458A ASP 5.3 0.2 - - - -
1462A LYS* 3.0 33.2 - - - +
6374F ASP* 3.3 9.0 + - - +
6375F GLN* 1.3 78.4 - - + +
6377F THR* 1.3 62.6 + - - +
6379F MET* 3.5 21.9 + - + +
6380F SER* 3.3 23.6 + - - -
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Residues in contact with THR6377 (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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1458A ASP 3.7 16.8 + - - +
1459A MET* 3.5 26.2 - - - +
1460A LYS 4.0 3.3 + - - -
1461A PRO* 3.8 15.6 - - + +
1462A LYS* 4.3 2.3 + - - +
6373F LEU* 3.4 23.1 - - + -
6374F ASP* 2.7 32.2 + - - -
6376F LYS* 1.3 75.2 - - - +
6378F ALA* 1.3 65.6 + - - +
6380F SER* 3.3 2.8 + - - -
6381F LEU* 3.0 25.9 + - + +
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Residues in contact with ALA6378 (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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6373F LEU* 4.0 10.5 - - + +
6374F ASP 3.0 10.6 + - - +
6375F GLN 3.3 9.6 - - - +
6376F LYS 3.2 0.2 - - - -
6377F THR* 1.3 77.8 - - - +
6379F MET* 1.3 57.9 + - - +
6381F LEU* 3.1 3.4 + - - +
6382F LEU* 2.8 30.8 + - - +
6400F THR* 3.9 7.0 - - + -
6404F LEU* 3.5 31.0 - - + -
6417F PHE* 3.5 21.1 - - + -
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Residues in contact with MET6379 (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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6375F GLN* 3.0 31.8 + - + +
6376F LYS* 3.7 25.1 - - + +
6377F THR 3.4 0.2 - - - -
6378F ALA* 1.3 75.4 - - - +
6380F SER* 1.3 61.9 + - - +
6383F TRP* 3.2 21.1 + - - +
6396F ILE* 3.6 23.5 - - + +
6397F PRO* 3.9 33.2 - - - +
6400F THR* 3.6 21.5 - - + +
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Residues in contact with SER6380 (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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1458A ASP* 3.4 39.8 + - - +
1459A MET* 4.6 4.0 - - - -
6376F LYS 3.3 11.9 + - - -
6377F THR 3.3 8.9 + - - -
6378F ALA 3.1 0.6 - - - -
6379F MET* 1.3 79.1 - - - +
6381F LEU* 1.3 62.5 + - - +
6383F TRP* 3.4 7.0 + - - +
6384F LYS* 3.2 27.3 + - - +
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Residues in contact with LEU6381 (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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1459A MET* 4.0 30.3 - - + +
6306F LEU* 5.9 0.7 - - + -
6366F TYR* 4.2 6.9 - - + +
6367F PRO* 3.8 29.8 - - + +
6368F LEU* 3.8 31.4 - - + -
6373F LEU* 3.9 19.1 - - + -
6377F THR* 3.0 23.6 + - + +
6378F ALA 3.6 5.6 - - - +
6380F SER* 1.3 74.2 - - - +
6382F LEU* 1.3 60.0 + - - +
6384F LYS* 3.3 8.7 + - + +
6385F SER* 2.8 33.5 + - - -
6417F PHE* 3.9 13.5 - - + -
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Residues in contact with LEU6382 (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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6378F ALA 2.8 16.1 + - - +
6379F MET* 3.9 5.2 - - - +
6381F LEU* 1.3 77.5 - - - +
6383F TRP* 1.3 62.1 + - - +
6385F SER* 3.2 14.1 + - - -
6386F TYR* 3.5 7.8 + - - -
6389F VAL* 3.8 13.9 - - + +
6391F ILE* 3.7 36.2 - - + +
6396F ILE* 3.8 28.7 - - + +
6399F ALA* 4.3 12.1 - - + -
6400F THR* 3.9 11.2 - - - +
6417F PHE* 4.0 16.5 - - + -
6420F LEU* 3.9 22.4 - - + -
6421F ILE* 4.6 6.7 - - + -
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Residues in contact with TRP6383 (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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6311F ASP* 4.3 1.8 - - - -
6312F PRO* 3.2 42.1 - - + +
6313F ARG* 3.5 44.2 - - + -
6379F MET 3.2 9.1 + - - +
6380F SER* 3.6 10.3 - - - +
6381F LEU 3.2 0.6 - - - -
6382F LEU* 1.3 75.4 - - - +
6384F LYS* 1.3 73.7 + - + +
6386F TYR* 3.0 36.6 + + - +
6391F ILE 3.9 8.7 - - - -
6392F ALA* 4.1 0.4 - - - -
6393F LYS* 3.3 64.0 - - + +
6396F ILE* 3.5 26.0 - - + +
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Residues in contact with LYS6384 (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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1459A MET* 4.2 26.7 - - + -
6306F LEU* 3.2 30.8 - - + +
6307F ASP 4.3 13.1 - - - +
6308F LEU* 3.1 30.9 + - + +
6310F GLY 3.2 27.1 + - - +
6312F PRO* 3.9 17.8 - - + +
6315F SER* 5.5 0.7 + - - -
6380F SER 3.2 14.4 + - - +
6381F LEU* 3.3 10.7 + - + +
6383F TRP* 1.3 85.0 - - + +
6385F SER* 1.3 57.9 + - - +
6386F TYR 3.1 3.4 + - - -
6387F PRO* 3.4 8.5 - - - +
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Residues in contact with SER6385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6306F LEU* 4.2 7.1 - - - +
6366F TYR* 2.6 40.3 + - - -
6381F LEU 2.8 16.5 + - - -
6382F LEU* 3.5 15.0 - - - -
6383F TRP 3.0 0.8 - - - -
6384F LYS* 1.3 74.5 - - - +
6386F TYR* 1.3 63.9 + - - +
6387F PRO* 3.2 4.7 - - - -
6388F LEU* 2.8 22.5 + - - +
6389F VAL* 3.0 17.9 + - - +
6421F ILE* 4.8 4.9 - - - -
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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