Contacts of the strand formed by residues 314 - 319 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A MET* 6.1 0.4 - - + -
307A SER* 3.6 18.3 + - - -
310A SER* 5.3 0.5 + - - -
312A ARG* 3.0 19.4 + - - +
313A PHE* 1.3 74.3 + - - +
315A TRP* 1.3 67.7 + - - +
358A GLU* 2.9 7.7 - - - +
359A PHE* 2.7 39.7 + - - +
373A LYS* 5.0 0.4 - - - -
374A PHE* 3.0 29.5 - - + +
375A TRP* 3.3 12.1 - - - +
376A ILE* 3.5 24.0 - - + +
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Residues in contact with TRP 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ARG 3.2 26.8 + - - -
277A TRP* 3.4 28.8 - + + +
280A SER* 3.7 12.6 - - - -
291A LEU* 4.6 6.7 - - + -
292A VAL* 4.3 4.3 - - - +
314A THR* 1.3 87.9 - - - +
316A MET* 1.3 61.8 + - - +
356A CYS* 3.3 37.9 - - + -
357A ALA 3.3 20.6 - - - -
358A GLU* 4.1 2.7 - - + -
359A PHE* 4.4 2.3 - - - -
367A ASP* 4.0 4.3 - - + -
368A LYS 3.2 30.1 - - - -
369A CYS* 4.0 7.9 - - - -
371A LEU 3.2 16.3 + - - -
373A LYS* 3.5 42.5 - - + +
374A PHE 2.7 15.4 + - - +
375A TRP* 4.3 9.2 - - + -
376A ILE 4.2 8.7 + - - -
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Residues in contact with MET 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TRP* 2.7 26.7 + - - -
291A LEU* 4.0 7.4 - - - -
292A VAL* 3.9 22.0 - - + +
294A ILE* 4.7 1.3 - - + -
315A TRP* 1.3 75.9 - - - +
317A GLY* 1.3 57.3 + - - +
318A LEU* 2.8 23.4 + - + -
329A TRP* 4.3 14.6 - - + -
357A ALA* 3.1 28.3 + - + +
358A GLU 3.8 22.2 - - - +
359A PHE* 3.5 37.2 - - + -
364A TRP* 3.9 27.1 - - + +
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Residues in contact with GLY 317 (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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277A TRP* 3.8 2.0 - - - -
291A LEU* 3.4 24.1 + - - +
292A VAL 3.2 11.8 + - - -
316A MET* 1.3 70.4 - - - +
318A LEU* 1.3 55.9 + - - -
329A TRP* 3.0 14.6 - - - +
330A VAL* 2.7 49.2 + - - +
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Residues in contact with LEU 318 (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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277A TRP* 3.6 4.3 - - - -
316A MET* 2.8 23.1 + - + +
317A GLY* 1.3 74.4 - - - +
319A SER* 1.3 72.1 + - - +
327A TRP* 3.5 34.5 - - + +
328A GLN 3.4 18.6 - - - +
329A TRP* 4.0 27.1 - - + +
335A LEU* 4.1 9.0 - - + -
343A TRP* 4.8 5.4 - - + -
356A CYS* 3.6 1.0 - - - -
357A ALA* 3.0 35.4 + - + -
364A TRP* 3.6 35.0 - - + -
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Residues in contact with SER 319 (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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277A TRP* 3.5 25.2 - - - -
318A LEU* 1.3 76.6 - - - +
320A ASP* 1.3 57.4 + - - +
321A LEU* 3.5 20.5 + - - +
326A THR 3.8 0.2 - - - +
327A TRP* 3.1 11.7 - - - -
328A GLN* 3.0 35.1 + - - +
355A ASP 2.8 21.5 - - - -
356A CYS* 4.0 1.8 - - - -
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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