Contacts of the helix formed by residues 6172 - 6178 (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 LEU6172 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6087F CYS* 4.1 15.4 - - + +
6088F THR 4.4 6.9 - - - +
6089F GLN* 3.4 30.1 - - + +
6140F HIS* 4.0 4.3 - - + +
6144F LEU 3.6 14.4 - - - +
6145F MET 3.7 9.4 - - - +
6146F VAL* 3.5 28.7 - - - +
6147F GLY 3.6 6.5 - - - +
6170F TYR* 3.4 48.2 - - + +
6171F ARG* 1.3 73.8 - - - +
6173F GLY* 1.3 69.6 + - - +
6175F TRP* 3.3 19.5 + - - +
6176F GLY* 3.1 9.3 + - - -
6177F PHE* 4.4 0.2 - - - -
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Residues in contact with GLY6173 (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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6144F LEU 2.8 15.2 + - - -
6145F MET* 3.7 33.1 - - - +
6172F LEU* 1.3 69.9 - - - +
6174F ILE* 1.3 57.7 + - - -
6175F TRP* 4.9 2.0 - - - -
6176F GLY 3.0 0.3 + - - -
6177F PHE* 2.6 39.0 + - - +
6298F THR* 6.4 0.2 - - - -
6319F LEU* 3.7 7.4 - - - -
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Residues in contact with ILE6174 (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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6065F PHE* 3.3 23.3 - - + -
6145F MET* 5.1 1.0 - - - +
6172F LEU 3.5 0.4 + - - -
6173F GLY* 1.3 70.7 - - - -
6175F TRP* 1.3 74.3 + - + +
6178F PHE* 3.0 39.8 + - + +
6268F ILE* 4.2 16.2 - - + -
6286F LEU* 5.6 1.3 - - + -
6294F LEU* 3.8 29.8 - - + +
6297F THR* 4.2 20.6 - - + -
6298F THR* 3.5 26.9 + - - +
6303F PHE* 4.8 9.2 - - + -
6319F LEU* 3.4 21.0 - - + +
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Residues in contact with TRP6175 (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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6059F PRO 6.0 1.1 - - - -
6064F ARG* 4.1 19.9 - - + +
6065F PHE* 4.1 11.9 + - - -
6087F CYS* 6.5 0.4 - - + -
6088F THR* 3.3 53.2 - - + -
6089F GLN* 4.7 2.7 - - - -
6114F GLU* 2.9 37.2 + - + +
6171F ARG* 3.8 30.0 + - + -
6172F LEU 3.5 15.7 - - - +
6173F GLY* 3.2 1.7 - - - -
6174F ILE* 1.3 84.4 - - + +
6176F GLY* 1.3 59.3 + - - +
6189F TRP* 3.5 14.6 - - - +
6291F GLU* 3.7 9.4 - - + -
6294F LEU* 3.3 34.2 - - + +
6295F LEU* 3.7 20.6 - - + -
6298F THR* 3.9 15.3 - - + -
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Residues in contact with GLY6176 (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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6171F ARG* 3.3 32.5 - - - +
6172F LEU 3.1 6.9 + - - -
6173F GLY 3.0 4.5 + - - -
6175F TRP* 1.3 79.0 - - - +
6177F PHE* 1.3 66.1 + - - +
6189F TRP* 2.9 30.2 + - - -
6190F GLY 2.9 7.9 + - - -
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Residues in contact with PHE6177 (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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6144F LEU* 3.8 44.4 - - + -
6170F TYR* 4.5 3.4 - + - -
6171F ARG 3.4 18.6 - - - -
6172F LEU* 4.4 0.4 - - - -
6173F GLY 2.6 19.0 + - - +
6176F GLY* 1.3 81.9 - - - +
6178F PHE* 1.3 65.2 + - - +
6179F SER* 3.1 10.2 + - - -
6187F GLY* 4.6 1.2 - - - -
6188F ASN* 4.1 15.9 + - - +
6189F TRP* 4.4 1.1 - - - -
6190F GLY* 3.8 15.9 - - - -
6191F HIS* 3.7 35.4 - + - -
6319F LEU* 3.4 36.2 - - + +
6320F GLY 3.6 28.5 - - - +
6321F THR 4.0 0.4 - - - -
6322F VAL* 5.2 1.0 - - - +
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Residues in contact with PHE6178 (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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6065F PHE* 3.8 22.0 - + + -
6173F GLY 4.0 0.2 + - - -
6174F ILE* 3.0 25.5 + - + +
6176F GLY 4.0 0.4 - - - -
6177F PHE* 1.3 74.9 - - - +
6179F SER* 1.3 60.0 + - - +
6180F THR* 3.6 31.2 - - + -
6185F SER* 3.1 27.0 + - - -
6187F GLY* 3.7 2.1 - - - -
6189F TRP* 3.2 14.9 + - - -
6265F ALA* 3.8 35.4 - - + -
6268F ILE* 4.1 23.1 - - + -
6282F MET* 4.8 6.7 - - + -
6283F VAL* 4.0 10.8 - - + -
6286F LEU* 3.3 33.9 - - + -
6319F LEU* 4.3 7.2 - - - +
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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