Contacts of the strand formed by residues 384 - 392 (chain C) in PDB entry 3KYS
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 384 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261C LEU* 3.5 25.2 - - + +
264C LYS* 3.7 12.2 + - - +
265C GLY* 4.5 16.4 - - - -
266C PRO* 3.9 16.2 - - - +
269C ALA* 4.3 2.6 - - + +
270C PHE* 4.2 23.2 - - + -
375C VAL* 4.5 7.4 - - + +
376C VAL 4.1 4.3 - - - +
377C THR* 4.5 4.7 + - - -
382C GLN 3.7 2.5 + - - -
383C GLU* 1.3 83.0 - - - +
385C LEU* 1.3 63.3 + - - +
386C LEU 3.8 24.2 - - - +
387C CYS* 4.2 4.3 - - + -
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Residues in contact with LEU 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C THR* 3.9 17.7 + - - +
200C LYS* 4.4 25.4 - - + -
201C LEU* 3.8 22.7 - - + +
269C ALA* 3.6 13.1 - - - +
303C MET* 3.8 38.1 - - + -
305C VAL* 4.0 16.4 - - + -
376C VAL 2.9 10.5 + - - +
377C THR 3.8 4.9 - - - +
378C ASN* 3.4 38.8 - - + +
383C GLU* 3.2 11.8 + - - +
384C THR* 1.3 74.1 - - - +
386C LEU* 1.3 63.1 + - - +
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Residues in contact with LEU 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C ILE* 3.1 34.8 - - + +
197C GLY* 3.8 13.2 - - - -
201C LEU* 4.1 19.1 - - + +
202C ARG 4.6 0.4 - - - -
203C LEU* 3.8 16.2 - - + +
269C ALA* 3.6 10.5 - - - +
271C PHE* 5.1 0.9 - - + -
297C TYR* 4.7 3.1 - - + -
374C LEU* 4.8 2.2 - - + +
375C VAL* 3.5 0.9 - - - -
376C VAL* 2.8 50.2 + - + +
384C THR* 3.6 4.2 - - - +
385C LEU* 1.3 80.2 - - - +
387C CYS* 1.3 67.8 - - - +
388C MET* 3.5 32.8 - - + -
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Residues in contact with CYS 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C LEU* 4.3 8.1 - - - -
261C LEU* 4.7 2.9 - - - -
269C ALA 2.8 10.7 + - - +
270C PHE* 3.4 39.0 - - + -
271C PHE* 2.9 28.4 + - - +
373C LEU* 3.7 25.6 - - - -
374C LEU 3.3 6.3 - - - +
375C VAL* 4.1 11.4 - - + -
384C THR* 4.2 8.1 - - + -
386C LEU* 1.3 78.8 - - - +
388C MET* 1.3 64.6 + - - +
389C ALA* 4.1 1.1 - - - -
408C LEU* 6.1 0.2 - - - -
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Residues in contact with MET 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C ILE* 4.1 12.3 - - + -
203C LEU* 3.4 34.8 - - + -
206C PHE* 6.1 1.8 - - - -
227C ILE* 4.4 7.0 - - - -
271C PHE* 3.5 8.7 - - + +
273C VAL* 3.6 32.5 - - + -
275C PHE* 5.3 1.6 - - - -
373C LEU* 3.8 2.4 - - - -
374C LEU* 2.7 56.7 + - + +
386C LEU* 3.5 24.5 - - + -
387C CYS* 1.3 73.7 - - - +
389C ALA* 1.3 60.8 + - - +
390C CYS* 3.6 19.6 - - - -
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Residues in contact with ALA 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C ILE* 4.8 1.6 - - + -
251C PHE* 3.5 30.1 - - + -
258C LEU* 4.7 5.4 - - + -
271C PHE 2.8 15.2 + - - +
272C LEU* 3.3 14.0 - - + +
273C VAL* 2.8 31.5 + - - -
372C ILE 3.9 1.1 - - - -
373C LEU* 4.0 11.4 - - + +
387C CYS* 4.1 1.0 - - - -
388C MET* 1.3 70.7 - - - +
390C CYS* 1.3 56.3 + - - +
408C LEU* 4.4 11.2 - - + -
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Residues in contact with CYS 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C PHE* 6.5 0.9 - - - -
251C PHE* 3.6 1.6 - - - -
273C VAL* 3.5 4.0 - - - -
275C PHE* 4.0 20.4 - - + -
371C THR* 3.4 12.8 - - - -
372C ILE* 2.8 45.5 + - + +
374C LEU* 5.0 4.5 - - - -
388C MET* 3.6 34.8 - - - -
389C ALA* 1.3 74.7 - - - +
391C VAL* 1.3 63.7 + - - +
392C PHE* 3.8 22.9 - - + -
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Residues in contact with VAL 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C ILE* 5.2 0.9 - - + -
250C LYS* 4.5 6.1 - - + -
251C PHE* 4.9 4.3 - - + -
272C LEU* 3.9 20.4 - - + -
273C VAL 3.0 9.7 + - - +
274C LYS* 3.5 11.8 - - + +
275C PHE* 2.7 33.1 + - - +
367C LEU 5.9 1.6 - - - +
370C PHE 4.9 3.8 - - - +
371C THR* 4.2 15.3 - - + -
390C CYS* 1.3 79.5 - - - +
392C PHE* 1.3 67.2 + - - +
393C GLU* 6.1 0.4 - - + -
86D MET* 3.9 23.3 - - + -
95D PHE* 3.9 24.9 - - + -
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Residues in contact with PHE 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C VAL* 4.4 4.7 - - + -
274C LYS* 4.3 2.0 - - - -
275C PHE* 3.3 46.2 - + + -
277C ALA* 4.8 5.6 - - + -
344C P1L 3.6 46.4 - - + -
367C LEU* 3.4 41.9 + - + +
370C PHE* 3.6 34.4 + + - +
372C ILE* 3.9 14.1 - - + -
390C CYS* 3.8 26.5 - - + -
391C VAL* 1.3 81.4 - - - +
393C GLU* 1.3 66.9 + - - +
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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