Contacts of the helix formed by residues 6395 - 6405 (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 LEU6395 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6391F ILE* 3.9 10.8 - - + -
6392F ALA* 2.8 29.1 + - + +
6394F GLU* 1.3 85.7 - - + +
6396F ILE* 1.3 63.5 + - - +
6397F PRO* 3.3 3.1 - - - -
6398F GLU* 3.3 10.3 + - - +
6399F ALA* 2.9 22.0 + - - +
6550F LEU* 3.9 52.1 - - + +
6551F PHE* 4.5 16.8 - - + +
6553F LYS* 4.4 19.5 - - + -
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Residues in contact with ILE6396 (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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6379F MET* 3.6 38.4 - - + +
6382F LEU* 3.8 11.4 - - + -
6383F TRP* 3.5 56.8 - - + +
6391F ILE* 3.9 17.0 - - + +
6392F ALA 3.4 11.4 + - - +
6393F LYS* 3.4 11.8 + - + +
6395F LEU* 1.3 77.2 - - - +
6397F PRO* 1.3 70.8 - - + +
6399F ALA* 3.6 2.2 - - - +
6400F THR* 2.8 33.3 + - - +
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Residues in contact with PRO6397 (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* 5.4 0.3 - - - +
6379F MET* 3.9 26.5 - - - +
6393F LYS 3.5 12.1 - - - +
6394F GLU 3.8 9.0 - - - +
6395F LEU 3.5 3.6 - - - -
6396F ILE* 1.3 94.1 - - + +
6398F GLU* 1.3 56.4 + - - +
6400F THR* 3.8 1.0 - - - -
6401F GLU* 2.8 32.3 + - - +
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Residues in contact with GLU6398 (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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6394F GLU 5.3 1.1 + - - +
6395F LEU* 3.3 12.2 + - - +
6397F PRO* 1.3 78.7 - - - +
6399F ALA* 1.3 64.7 + - - +
6401F GLU* 3.6 7.0 - - + +
6402F LYS* 2.9 26.4 + - + +
6546F PHE* 3.8 16.9 - - + -
6550F LEU* 3.2 26.2 - - + +
6553F LYS* 2.6 33.3 + - - +
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Residues in contact with ALA6399 (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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6382F LEU* 4.3 13.0 - - + -
6391F ILE* 4.5 2.5 - - + -
6395F LEU 2.9 17.9 + - - +
6396F ILE* 3.6 5.4 - - - +
6398F GLU* 1.3 79.0 - - - +
6400F THR* 1.3 62.0 + - - +
6402F LYS* 3.4 3.8 + - - +
6403F TYR* 3.3 24.9 + - - -
6420F LEU* 3.8 3.6 - - + +
6546F PHE* 4.0 13.0 - - - -
6547F TRP* 3.8 26.9 - - + -
6550F LEU* 4.0 7.3 - - + +
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Residues in contact with THR6400 (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* 4.1 13.7 - - + +
6378F ALA* 3.9 14.4 - - + -
6379F MET* 3.6 24.0 - - + +
6382F LEU* 3.9 9.4 - - - +
6396F ILE* 2.8 25.0 + - - +
6397F PRO 3.8 2.7 - - - -
6399F ALA* 1.3 70.6 - - - +
6401F GLU* 1.3 59.5 + - - +
6403F TYR 3.2 0.5 + - - -
6404F LEU* 2.7 61.7 + - + +
6417F PHE* 5.5 2.5 - - + -
6420F LEU* 4.3 8.8 - - - +
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Residues in contact with GLU6401 (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* 3.8 15.7 + - - +
6397F PRO 2.8 19.7 + - - +
6398F GLU* 3.6 8.3 - - + +
6400F THR* 1.3 74.4 - - - +
6402F LYS* 1.3 62.5 + - - +
6405F GLY* 2.8 58.4 + - - +
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Residues in contact with LYS6402 (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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6398F GLU* 2.9 17.6 + - + +
6399F ALA 3.6 5.8 - - - +
6401F GLU* 1.3 78.9 - - - +
6403F TYR* 1.3 66.5 + - + +
6406F GLY 5.5 1.4 + - - -
6542F LYS 6.0 0.4 - - - -
6546F PHE* 3.6 49.9 - - + -
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Residues in contact with TYR6403 (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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6399F ALA 3.3 12.2 + - - +
6400F THR 3.2 2.7 + - - +
6402F LYS* 1.3 91.6 - - + +
6404F LEU* 1.3 64.0 + - + +
6405F GLY 3.7 0.2 - - - -
6406F GLY* 4.7 2.1 + - - -
6416F LEU* 3.1 44.9 - - + +
6419F ASP* 4.0 6.3 - - + -
6420F LEU* 3.5 46.7 - - + -
6423F ASP* 2.6 30.5 + - - -
6543F GLU* 3.5 12.3 - - + +
6546F PHE* 4.4 8.7 - + - -
6547F TRP* 3.0 39.2 + + - -
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Residues in contact with LEU6404 (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* 5.1 1.1 - - + -
6374F ASP 4.9 0.7 - - - +
6375F GLN* 3.7 20.6 - - + +
6378F ALA* 3.5 32.3 - - + -
6400F THR* 2.7 30.1 + - + +
6403F TYR* 1.3 77.2 - - + +
6405F GLY* 1.3 52.6 + - - +
6406F GLY* 2.5 19.3 + - - -
6407F THR* 3.4 17.3 + - - +
6413F LYS* 3.0 49.2 - - + +
6416F LEU* 3.5 14.5 - - + +
6417F PHE* 3.4 24.0 - - + +
6420F LEU* 5.8 0.4 - - + -
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Residues in contact with GLY6405 (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* 3.3 14.0 - - - +
6400F THR 3.7 0.4 + - - -
6401F GLU* 2.8 38.0 + - - +
6404F LEU* 1.3 75.2 - - - +
6406F GLY* 1.3 59.2 + - - +
6407F THR 3.6 2.9 - - - -
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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