Contacts of the helix formed by residues 6357 - 6364 (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 TRP6357 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1367A PRO* 3.8 20.8 + - + +
1369A SER* 3.6 20.7 + - - -
1370A GLU* 4.8 3.8 - - + -
6100F LEU* 4.7 3.8 - - + -
6355F PHE 3.5 2.2 - - - -
6356F GLY* 1.3 78.1 - - - +
6358F LEU* 1.3 91.0 + - + +
6359F ILE 3.5 1.8 - - - -
6360F PRO* 3.3 4.1 - - - +
6361F MET* 2.9 64.4 + - + +
6457F SER* 3.8 32.1 - - - -
6459F MET* 3.6 37.6 + - + -
6460F LYS* 3.8 22.0 - - + -
6461F PRO* 3.8 16.7 - - + +
6464F VAL* 4.2 11.7 - - + -
6467F ASP* 3.1 16.1 + - - +
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Residues in contact with LEU6358 (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 4.9 3.6 - - + +
6097F LEU* 5.5 0.4 - - + -
6100F LEU* 3.6 33.2 - - + -
6101F PHE* 4.1 27.8 - - + -
6357F TRP* 1.3 90.3 - - + +
6359F ILE* 1.3 75.4 + - + +
6361F MET* 3.5 1.9 - - + +
6363F LEU* 3.0 48.9 + - + +
6467F ASP* 2.8 26.0 + - - +
6468F HIS* 4.0 21.3 - - + +
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Residues in contact with ILE6359 (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 4.0 23.6 - - - +
6354F GLU 3.5 21.1 + - - +
6355F PHE* 3.4 26.0 - - + -
6358F LEU* 1.3 77.1 - - + +
6360F PRO* 1.3 72.8 - - + +
6363F LEU* 3.2 5.8 + - - +
6364F MET* 2.9 40.1 + - + +
6425F MET* 5.1 1.3 - - + -
6426F PHE* 3.7 27.1 - - + -
6467F ASP* 5.0 0.8 + - - -
6468F HIS* 3.7 31.6 - - + -
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Residues in contact with PRO6360 (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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1369A SER* 3.8 22.0 - - - +
6355F PHE* 3.3 51.1 - - + +
6357F TRP* 3.3 15.7 - - - +
6359F ILE* 1.3 96.5 - - + +
6361F MET* 1.3 59.8 + - - +
6364F MET* 3.3 2.0 + - + -
6365F SER 3.1 3.5 + - - -
6366F TYR* 2.9 50.1 + - + +
6418F LEU* 5.2 2.2 - - + -
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Residues in contact with MET6361 (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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1308A LEU* 3.6 11.7 - - + -
1365A SER 5.4 0.7 - - - +
1367A PRO* 3.6 35.7 - - + -
1369A SER* 4.7 4.2 + - - +
6F COA 3.4 35.0 + - - +
6096F LEU* 4.5 4.3 - - + -
6100F LEU* 3.7 22.2 - - + -
6357F TRP* 2.9 51.0 + - + +
6358F LEU* 3.5 2.7 - - + +
6360F PRO* 1.3 77.2 - - - +
6363F LEU* 1.3 92.6 + - + +
6365F SER* 3.2 12.6 + - - +
6459F MET* 5.8 0.7 - - + -
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Residues in contact with LEU6363 (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 2.7 97.5 + - + +
6096F LEU* 3.6 17.5 - - + -
6097F LEU* 4.4 3.4 - - + +
6100F LEU* 4.4 2.2 - - + -
6304F LEU 3.8 1.6 - - - +
6305F SER* 5.4 0.2 + - - -
6358F LEU* 3.0 44.2 + - + +
6359F ILE* 3.7 4.7 - - - +
6361F MET* 1.3 100.6 - - + +
6364F MET* 1.3 61.1 + - + +
6365F SER* 3.2 1.1 + - - -
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Residues in contact with MET6364 (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 4.9 13.7 - - + +
6304F LEU* 3.8 17.3 - - + +
6305F SER* 3.8 26.6 - - - +
6306F LEU* 3.0 30.9 + - + +
6317F PRO* 3.9 21.3 - - + -
6318F LEU* 5.3 3.8 - - + -
6355F PHE* 5.4 0.9 - - + -
6359F ILE* 2.9 34.2 + - + +
6360F PRO* 3.3 3.6 + - + +
6361F MET 3.2 0.2 - - - -
6363F LEU* 1.3 78.2 - - + +
6365F SER* 1.3 69.5 + - - +
6366F TYR* 3.1 6.8 + - + +
6387F PRO* 6.5 0.2 - - + -
6388F LEU* 3.9 40.2 - - + -
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Residues in contact with SER6365 (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 3.6 33.4 + - - -
1361A MET* 5.3 1.9 - - - +
1365A SER* 2.7 40.1 + - - +
6F COA 4.1 16.3 + - - -
6305F SER* 4.3 2.7 + - - -
6306F LEU* 4.8 0.7 - - - +
6360F PRO 3.1 3.9 + - - -
6361F MET* 3.2 9.7 + - - +
6363F LEU 3.2 1.8 + - - -
6364F MET* 1.3 80.1 - - - +
6366F TYR* 1.3 66.4 + - - +
6367F PRO* 3.4 9.2 - - - +
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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