Contacts of the strand formed by residues 314 - 319 (chain F) in PDB entry 1K9I
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 THR 314 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307F SER* 3.6 10.5 + - - -
312F ARG* 3.3 16.7 + - - +
313F PHE* 1.3 77.4 + - - +
315F TRP* 1.3 64.9 + - - +
358F GLU* 3.0 7.1 + - - -
359F PHE* 2.7 47.4 + - + +
374F PHE* 3.3 8.9 - - + +
375F TRP* 3.3 39.7 - - - +
376F ILE* 3.7 17.6 - - + +
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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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275F ARG 3.1 21.0 + - - -
277F TRP* 3.4 31.8 - + + +
280F SER* 3.4 21.5 - - - +
291F LEU* 3.7 15.4 - - + +
292F VAL* 4.3 3.1 - - - +
314F THR* 1.3 84.8 - - - +
316F MET* 1.3 60.5 + - - +
356F CYS* 3.2 37.5 - - + -
357F ALA 3.4 20.0 - - - -
358F GLU* 4.0 4.9 - - + -
359F PHE* 4.4 1.1 - - - -
367F ASP* 4.2 3.4 - - + -
368F LYS 3.3 25.4 - - - -
369F CYS* 4.1 6.3 - - - -
371F LEU 3.4 16.5 + - - -
373F LYS* 3.5 42.7 - - + +
374F PHE 2.9 14.4 + - - +
375F TRP* 4.2 7.6 - - + -
376F ILE 3.7 4.2 + - - -
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Residues in contact with MET 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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277F TRP* 3.0 18.4 + - - -
291F LEU* 3.7 5.8 - - - -
292F VAL* 3.7 15.9 - - + +
294F ILE* 3.9 10.1 - - + -
314F THR 3.8 0.2 + - - -
315F TRP* 1.3 72.6 - - - +
317F GLY* 1.3 59.1 + - - +
318F LEU* 2.8 28.5 + - + -
329F TRP* 3.9 22.7 - - + -
357F ALA* 3.2 16.8 + - + +
358F GLU 3.7 26.9 - - - +
359F PHE* 3.7 24.9 - - + -
364F TRP* 3.6 39.5 - - + +
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Residues in contact with GLY 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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277F TRP* 4.2 0.7 - - - -
291F LEU* 3.4 31.4 + - - -
292F VAL 2.8 15.3 + - - -
316F MET* 1.3 67.7 - - - +
318F LEU* 1.3 58.2 + - - -
329F TRP* 3.2 14.0 - - - -
330F VAL* 2.8 41.0 + - - +
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Residues in contact with LEU 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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277F TRP* 4.0 3.6 + - - -
316F MET* 2.8 17.3 + - + +
317F GLY* 1.3 74.8 - - - +
319F SER* 1.3 65.7 + - - +
327F TRP* 3.7 22.2 - - + -
328F GLN 3.4 33.2 - - - +
329F TRP* 3.7 31.9 - - + +
335F LEU* 4.1 11.7 - - + -
343F TRP* 4.6 1.1 - - + -
356F CYS* 3.8 0.9 - - - -
357F ALA* 3.0 40.7 + - + +
364F TRP* 3.6 32.5 - - + -
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Residues in contact with SER 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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277F TRP* 3.8 21.7 - - - -
318F LEU* 1.3 78.0 - - - +
320F ASP* 1.3 59.8 + - - +
321F LEU* 3.5 23.9 + - - +
326F THR 3.9 0.3 - - - +
327F TRP* 3.3 12.0 - - - -
328F GLN* 2.8 43.9 + - - +
355F ASP 2.9 17.5 - - - -
356F CYS* 4.1 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