Contacts of the helix formed by residues 372 - 380 (chain F) in PDB entry 3KHU
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 PRO 372 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343F GLY* 4.4 9.4 - - - +
370F LYS 3.3 8.5 - - - +
371F VAL* 1.3 91.0 - - + +
373F ARG* 1.3 65.2 + - - +
374F GLU* 4.4 6.3 - - + +
375F GLN* 3.1 24.7 + - + +
376F ILE* 3.4 8.4 + - - +
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Residues in contact with ARG 373 (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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371F VAL 3.7 2.2 + - - -
372F PRO* 1.3 71.8 - - - +
374F GLU* 1.3 69.8 + - + +
376F ILE* 3.2 9.6 + - - +
377F VAL* 3.1 42.1 + - - +
397F ILE* 3.7 52.6 + - + +
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Residues in contact with GLU 374 (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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372F PRO* 3.2 4.8 - - + +
373F ARG* 1.3 84.3 - - + +
375F GLN* 1.3 57.9 + - - +
377F VAL* 3.5 10.0 + - - +
378F VAL* 3.1 33.3 + - + +
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Residues in contact with GLN 375 (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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343F GLY 5.3 1.8 - - - +
345F THR* 3.8 19.5 + - + +
346F ARG* 6.4 0.2 - - - +
371F VAL* 4.3 6.1 - - + -
372F PRO* 3.1 22.8 + - + +
374F GLU* 1.3 76.5 - - - +
376F ILE* 1.3 60.0 + - - +
378F VAL* 3.2 16.3 + - - +
379F ASP* 2.8 68.1 + - - +
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Residues in contact with ILE 376 (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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336F PHE* 3.8 28.3 - - + -
366F ILE* 3.9 37.5 - - + +
368F ASP* 5.0 6.5 - - + +
371F VAL* 3.5 32.3 - - + +
372F PRO 3.4 5.8 + - - +
373F ARG* 3.2 8.2 + - - +
375F GLN* 1.3 75.7 - - - +
377F VAL* 1.3 63.5 + - - +
379F ASP* 3.4 0.7 + - - +
380F LEU* 3.2 27.2 + - + +
395F VAL* 5.0 0.4 - - + -
397F ILE* 3.3 40.6 - - + -
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Residues in contact with VAL 377 (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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373F ARG* 3.1 35.8 + - - +
374F GLU* 3.7 11.2 - - - +
376F ILE* 1.3 79.5 - - - +
378F VAL* 1.3 60.0 + - + +
380F LEU* 3.4 2.1 + - - +
381F SER* 2.7 40.6 + - - +
391F VAL* 4.2 22.3 - - + +
395F VAL* 5.7 1.1 - - + -
397F ILE* 4.5 11.7 - - + -
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Residues in contact with VAL 378 (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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374F GLU* 3.1 20.7 + - + +
375F GLN* 3.6 22.0 - - - +
377F VAL* 1.3 77.7 - - + +
379F ASP* 1.3 66.1 + - - +
381F SER* 3.1 24.3 + - - +
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Residues in contact with ASP 379 (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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336F PHE* 3.6 14.8 - - + -
345F THR* 2.5 36.2 + - - +
351F ILE* 3.9 28.5 - - + +
355F LYS* 3.9 17.5 + - - -
375F GLN* 2.8 39.6 + - - +
376F ILE 3.8 4.3 - - - +
377F VAL 3.3 0.2 - - - -
378F VAL* 1.3 79.0 - - - +
380F LEU* 1.3 61.2 + - - +
381F SER 3.6 1.9 + - - +
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Residues in contact with LEU 380 (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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336F PHE* 3.9 15.3 - - + -
351F ILE* 3.8 15.0 - - + +
354F SER* 3.8 24.0 - - - -
355F LYS* 4.3 20.1 - - + +
358F MET* 3.9 20.2 - - - +
366F ILE* 3.6 31.0 - - + -
376F ILE* 3.2 22.7 + - + +
377F VAL 4.2 0.2 - - - +
378F VAL 3.2 0.2 - - - -
379F ASP* 1.3 78.9 - - - +
381F SER* 1.3 59.7 + - - +
382F HIS* 4.2 4.0 + - - -
390F GLN* 5.3 1.0 - - - +
391F VAL* 3.0 24.4 - - + +
395F VAL* 3.9 18.8 - - + -
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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