Contacts of the helix formed by residues 6290 - 6302 (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 THR6290 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584F SO4 3.3 19.1 - - - +
6064F ARG* 4.2 0.9 - - - -
6288F GLN 5.0 3.6 - - - +
6289F LYS* 1.3 77.9 - - - +
6291F GLU* 1.3 65.2 + - - +
6292F GLU* 3.5 9.2 + - - +
6293F GLU* 2.8 45.6 + - - +
6294F LEU* 3.0 21.1 + - - +
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Residues in contact with GLU6291 (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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5275E LYS* 4.6 17.5 + - - -
584F SO4 2.9 19.3 + - - +
6088F THR* 2.7 39.7 + - + +
6112F LEU* 4.1 4.4 - - - +
6113F SER* 3.3 22.8 + - - -
6114F GLU* 3.4 36.3 + - + +
6175F TRP* 3.7 5.7 - - + -
6290F THR* 1.3 70.5 - - - +
6292F GLU* 1.3 60.6 + - - +
6294F LEU* 3.2 2.8 + - - -
6295F LEU* 2.9 30.1 + - + +
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Residues in contact with GLU6292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1300A LYS* 3.2 19.5 + - - +
6290F THR* 3.1 8.6 - - - +
6291F GLU* 1.3 82.7 - - - +
6293F GLU* 1.3 56.9 + - + +
6295F LEU* 3.3 22.9 + - - +
6296F GLU* 2.7 55.3 + - - +
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Residues in contact with GLU6293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6272F ALA* 6.3 0.2 - - - -
6288F GLN 4.5 0.7 - - - +
6289F LYS* 3.2 32.2 + - + +
6290F THR* 2.8 46.6 + - - +
6292F GLU* 1.3 77.7 - - + +
6294F LEU* 1.3 61.6 + - - +
6296F GLU* 3.4 15.3 + - - +
6297F THR* 3.0 26.6 + - - -
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Residues in contact with LEU6294 (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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6064F ARG* 3.1 43.3 - - - +
6065F PHE* 4.4 7.0 - - + -
6174F ILE* 3.8 19.9 - - + +
6175F TRP* 3.3 34.3 - - + +
6272F ALA* 5.0 0.9 - - + -
6286F LEU* 3.9 26.0 - - + +
6289F LYS* 3.9 17.9 - - + -
6290F THR 3.0 13.7 + - - +
6291F GLU 3.7 1.6 - - - +
6293F GLU* 1.3 73.8 - - - +
6295F LEU* 1.3 60.6 + - - +
6297F THR* 3.3 10.2 + - - +
6298F THR* 2.9 30.1 + - - -
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Residues in contact with LEU6295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6088F THR* 4.3 13.0 - - + -
6089F GLN* 3.7 26.2 - - - +
6090F ASP* 4.2 1.8 - - - +
6091F PRO* 4.4 7.0 - - + -
6112F LEU* 4.2 21.8 - - + -
6175F TRP* 3.7 10.2 - - + -
6291F GLU* 2.9 18.4 + - + +
6292F GLU* 3.5 26.7 - - - +
6294F LEU* 1.3 77.4 - - - +
6296F GLU* 1.3 62.6 + - - +
6298F THR* 3.0 7.8 + - - -
6299F LEU* 3.0 51.3 + - + +
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Residues in contact with GLU6296 (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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1296A GLU* 2.7 40.0 - - + +
1300A LYS* 2.7 42.9 + - + -
6292F GLU* 2.7 35.6 + - - +
6293F GLU* 3.6 16.3 - - - +
6294F LEU 3.3 0.2 - - - -
6295F LEU* 1.3 77.6 - - - +
6297F THR* 1.3 59.9 + - - +
6299F LEU* 3.3 9.9 + - + +
6300F LYS* 3.0 33.5 + - - +
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Residues in contact with THR6297 (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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6174F ILE* 4.2 12.6 - - + -
6268F ILE* 3.8 20.9 - - + +
6271F THR* 3.8 26.2 + - + -
6272F ALA* 3.5 26.1 - - + +
6293F GLU 3.0 16.1 + - - -
6294F LEU* 3.5 12.5 - - + -
6295F LEU 3.2 0.2 - - - -
6296F GLU* 1.3 76.9 - - - +
6298F THR* 1.3 60.5 + - - +
6300F LYS* 3.4 4.4 + - - +
6301F MET* 2.9 37.6 + - + +
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Residues in contact with THR6298 (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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6F COA 5.7 2.7 - - - +
6089F GLN* 5.7 2.0 - - - -
6090F ASP* 5.1 10.3 - - + +
6145F MET* 4.5 10.3 - - + -
6173F GLY* 6.4 0.4 - - - -
6174F ILE* 3.5 15.3 + - - +
6175F TRP* 3.9 14.7 - - + -
6294F LEU 2.9 17.1 + - - -
6295F LEU* 3.2 16.8 - - + -
6297F THR* 1.3 77.6 - - - +
6299F LEU* 1.3 69.9 + - + +
6301F MET* 3.3 13.2 + - - +
6302F LYS 3.4 8.0 + - - -
6303F PHE* 3.7 29.2 + - + -
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Residues in contact with LEU6299 (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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1A COA 3.2 17.9 + - - +
1299A LEU* 5.3 9.0 - - + -
1300A LYS* 3.9 32.8 - - + +
6F COA 4.0 31.2 + - - +
6090F ASP* 4.4 17.5 - - - +
6091F PRO* 5.2 4.5 - - + -
6295F LEU* 3.0 43.7 + - + +
6296F GLU* 3.3 13.7 + - + +
6298F THR* 1.3 82.8 - - + +
6300F LYS* 1.3 61.8 + - + +
6302F LYS* 3.1 12.4 + - - +
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Residues in contact with LYS6300 (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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1A COA 4.5 5.8 + - - -
1092A LYS* 3.2 21.7 + - - +
1292A GLU* 3.1 27.5 + - - +
1296A GLU* 2.9 38.4 + - - -
1299A LEU* 3.9 22.4 - - + -
6271F THR* 3.9 33.0 + - + +
6296F GLU* 3.0 27.6 + - - +
6297F THR* 3.8 4.7 - - - +
6298F THR 3.4 0.2 - - - -
6299F LEU* 1.3 75.7 - - - +
6301F MET* 1.3 61.2 + - - +
6302F LYS* 3.3 1.7 + - - +
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Residues in contact with MET6301 (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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1092A LYS* 3.6 5.2 + - - +
6174F ILE* 5.6 0.4 - - + -
6264F LEU* 4.1 4.3 - - + -
6267F GLN* 3.7 32.8 - - + +
6268F ILE* 3.8 23.6 - - + -
6271F THR* 3.5 27.8 - - + -
6297F THR* 2.9 33.8 + - + +
6298F THR 3.5 0.7 - - - +
6299F LEU 3.2 0.4 - - - -
6300F LYS* 1.3 75.2 - - - +
6302F LYS* 1.3 76.1 + - - +
6303F PHE* 3.4 49.3 + - + -
6316F GLN* 5.1 3.3 - - + +
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Residues in contact with LYS6302 (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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1A COA 2.7 41.8 - - + +
1092A LYS* 3.0 50.7 - - + +
6F COA 2.9 16.3 + - - +
6298F THR 3.4 2.2 + - - -
6299F LEU* 3.1 12.8 + - - +
6300F LYS 3.1 3.5 - - - +
6301F MET* 1.3 89.2 - - - +
6303F PHE* 1.3 60.4 + - - +
6305F SER* 3.7 13.9 + - - +
6306F LEU 6.4 0.2 - - - -
6307F ASP* 3.0 46.7 + - - +
6309F GLN* 5.4 3.4 - - - +
6316F GLN 5.2 0.9 - - - +
6317F PRO* 5.2 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