Contacts of the helix formed by residues 313 - 322 (chain F) in PDB entry 7KHI
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 ASP 313 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312F SER* 1.3 73.2 - - - +
314F THR* 1.3 55.9 + - - +
315F TRP 3.3 3.1 - - - -
316F PHE* 2.9 13.2 + - + -
317F ASN* 2.7 53.0 + - - +
338F HIS* 2.9 33.2 + - - -
341F LEU* 3.1 23.5 - - - +
345F GLN* 4.0 10.9 + - - +
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Residues in contact with THR 314 (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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305F LEU* 5.0 4.9 - - - +
309F ASN* 5.4 3.1 - - + +
312F SER* 3.3 20.5 + - - +
313F ASP* 1.3 75.9 - - - +
315F TRP* 1.3 75.9 + - + +
317F ASN* 3.9 4.0 - - - +
318F ALA* 2.9 31.6 + - - +
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Residues in contact with TRP 315 (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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287F ILE* 4.4 13.2 - - + -
291F CYS* 4.6 17.7 - - - -
302F PHE* 5.6 3.1 - + - -
305F LEU* 3.4 46.7 - - + +
306F PHE* 3.4 49.9 - + + +
309F ASN* 5.2 2.0 - - + -
310F GLU* 4.1 13.1 - - - +
312F SER* 2.8 22.7 + - - -
314F THR* 1.3 84.0 - - + +
316F PHE* 1.3 92.8 + + - +
318F ALA* 3.9 2.6 - - - +
319F ALA* 2.9 35.7 + - + +
337F VAL* 5.3 0.7 - - + -
341F LEU* 3.7 33.4 - - + -
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Residues in contact with PHE 316 (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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313F ASP* 2.9 23.5 + - + +
315F TRP* 1.3 109.8 - + + +
317F ASN* 1.3 70.8 + - - +
319F ALA* 3.3 4.0 + - - +
320F ILE* 3.0 49.6 + - + +
330F LEU* 3.5 36.0 - - + +
331F HIS* 5.8 1.1 - + - -
334F SER* 3.9 18.4 - - - -
337F VAL* 3.9 20.2 - - + -
338F HIS* 4.2 27.1 - + + -
341F LEU* 4.8 5.4 - - + -
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Residues in contact with ASN 317 (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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313F ASP* 2.7 43.7 + - - +
314F THR* 4.3 3.7 - - - +
316F PHE* 1.3 84.1 - - - +
318F ALA* 1.3 59.4 + - - +
320F ILE* 3.9 9.3 - - - +
321F ALA* 2.9 29.6 + - - +
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Residues in contact with ALA 318 (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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305F LEU* 4.0 25.1 - - + +
314F THR* 2.9 20.1 + - - +
315F TRP* 3.9 4.3 - - - +
317F ASN* 1.3 74.8 - - - +
319F ALA* 1.3 59.5 + - - +
321F ALA* 3.3 6.9 + - - +
322F MET* 2.8 28.5 + - - +
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Residues in contact with ALA 319 (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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297F MET* 4.6 14.1 - - + -
305F LEU* 4.8 4.8 - - + +
315F TRP* 2.9 22.7 + - + +
316F PHE* 3.6 4.7 - - - +
318F ALA* 1.3 76.4 - - - +
320F ILE* 1.3 61.2 + - - +
322F MET* 3.1 18.7 + - - +
326F TRP* 4.5 19.1 - - + -
327F SER* 2.8 23.1 + - - -
330F LEU* 4.6 8.1 - - + -
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Residues in contact with ILE 320 (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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316F PHE* 3.0 54.4 + - + +
317F ASN* 4.1 10.5 - - - +
319F ALA* 1.3 74.6 - - - +
321F ALA* 1.3 61.4 + - - +
322F MET 3.4 0.5 + - - -
323F ASN* 3.6 10.2 + - - -
327F SER* 4.0 18.6 - - - +
328F GLU* 5.8 0.7 - - - -
330F LEU* 3.7 23.6 - - + -
331F HIS* 3.8 32.5 - - + +
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Residues in contact with ALA 321 (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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317F ASN 2.9 20.9 + - - +
318F ALA* 3.5 7.9 - - - +
320F ILE* 1.3 71.8 - - - +
322F MET* 1.3 57.0 + - - +
323F ASN* 2.8 32.7 + - - +
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Residues in contact with MET 322 (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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297F MET* 5.2 8.1 - - - -
298F PRO* 5.4 8.1 - - + -
301F ASN* 4.5 22.2 - - + +
305F LEU* 5.9 5.4 - - - -
318F ALA 2.8 14.0 + - - +
319F ALA* 3.1 18.5 + - - +
321F ALA* 1.3 74.7 - - - +
323F ASN* 1.3 62.4 + - - +
324F LYS* 3.1 44.9 + - + +
326F TRP* 4.2 15.9 - - + -
327F SER* 4.4 1.6 - - - +
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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