Contacts of the helix formed by residues 372 - 380 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A GLY* 4.4 8.3 - - - +
370A LYS 3.3 8.7 - - - +
371A VAL* 1.3 92.0 - - + +
373A ARG* 1.3 65.7 + - - +
374A GLU* 4.4 7.0 - - + +
375A GLN* 3.1 24.9 + - + +
376A ILE* 3.4 8.2 + - - +
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Residues in contact with ARG 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A VAL 3.7 2.0 + - - -
372A PRO* 1.3 71.4 - - - +
374A GLU* 1.3 93.2 + - - +
376A ILE* 3.1 9.9 + - - +
377A VAL* 3.1 41.5 + - - +
397A ILE* 3.7 54.9 + - + +
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Residues in contact with GLU 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A PRO* 3.2 5.1 - - + +
373A ARG* 1.3 110.5 + - - +
375A GLN* 1.3 56.8 + - - +
377A VAL* 3.4 10.3 + - + +
378A VAL* 3.0 33.4 + - + +
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Residues in contact with GLN 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A GLY 5.3 1.8 - - - +
345A THR* 3.7 21.3 + - + +
346A ARG* 6.4 0.2 - - - +
371A VAL* 4.2 5.6 - - + -
372A PRO* 3.1 23.6 + - + +
374A GLU* 1.3 75.5 - - - +
376A ILE* 1.3 60.8 + - - +
378A VAL* 3.2 15.5 + - - +
379A ASP* 2.8 67.5 + - - +
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Residues in contact with ILE 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A PHE* 3.8 30.1 - - + -
366A ILE* 3.9 37.7 - - + +
368A ASP* 5.0 6.7 - - + +
371A VAL* 3.7 32.8 - - + +
372A PRO 3.4 5.6 + - - +
373A ARG* 3.1 6.8 + - - +
375A GLN* 1.3 75.5 - - - +
377A VAL* 1.3 62.1 + - - +
379A ASP* 3.4 0.7 + - - +
380A LEU* 3.1 27.2 + - + +
395A VAL* 5.0 0.2 - - + -
397A ILE* 3.4 39.9 - - + -
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Residues in contact with VAL 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A ARG* 3.1 36.2 + - - +
374A GLU* 3.6 12.6 - - + +
375A GLN 3.2 0.2 - - - -
376A ILE* 1.3 78.3 - - - +
378A VAL* 1.3 60.5 + - + +
380A LEU* 3.4 2.3 + - - +
381A SER* 2.7 39.4 + - - +
391A VAL* 4.3 22.5 - - + +
395A VAL* 5.7 1.8 - - + -
397A ILE* 4.6 11.2 - - + -
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Residues in contact with VAL 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A GLU* 3.0 21.1 + - + +
375A GLN* 3.2 21.5 + - - +
377A VAL* 1.3 78.9 - - + +
379A ASP* 1.3 65.3 + - - +
381A SER* 3.1 22.6 + - - +
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Residues in contact with ASP 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A PHE* 3.5 18.0 - - + -
345A THR* 2.6 35.6 + - - +
351A ILE* 4.0 26.1 - - + +
355A LYS* 3.9 17.2 + - - -
375A GLN* 2.8 41.9 + - - +
376A ILE 3.8 4.5 - - - +
378A VAL* 1.3 76.9 - - - +
380A LEU* 1.3 61.8 + - - +
381A SER 3.5 2.1 + - - +
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Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A PHE* 4.0 16.4 - - + -
351A ILE* 3.9 16.4 - - + +
354A SER* 3.8 22.7 - - - -
355A LYS* 4.2 18.1 - - + +
358A MET* 3.9 17.9 - - - +
366A ILE* 3.5 32.1 - - + -
376A ILE* 3.1 20.7 + - + +
377A VAL 3.7 0.9 - - - +
378A VAL 3.2 0.2 - - - -
379A ASP* 1.3 80.3 - - - +
381A SER* 1.3 59.0 + - - +
382A HIS* 5.2 0.3 + - - -
388A ASP* 3.8 5.4 - - - +
390A GLN* 5.4 0.2 - - - +
391A VAL* 3.0 25.2 - - + +
395A VAL* 4.0 17.9 - - + -
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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