Contacts of the strand formed by residues 288 - 299 (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 GLY 288 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211C GLU 3.6 0.3 - - - +
212C GLN* 3.1 7.2 - - - +
213C GLN* 2.8 43.8 + - - +
287C ALA* 1.3 77.3 - - - +
289C ALA* 1.3 60.5 + - - -
290C PHE 4.3 0.2 - - - -
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Residues in contact with ALA 289 (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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210C LEU* 3.9 18.4 - - + -
211C GLU 3.2 4.7 - - - +
212C GLN* 4.4 10.3 - - + +
283C ILE* 6.0 1.6 - - + -
284C GLN 4.9 7.0 - - - +
285C ASP* 5.8 4.0 - - - +
287C ALA 4.0 3.2 + - - +
288C GLY* 1.3 72.4 - - - -
290C PHE* 1.3 59.7 + - - +
291C TYR* 4.2 16.1 + - + +
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Residues in contact with PHE 290 (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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209C PHE* 3.9 14.9 - + - +
210C LEU* 3.5 1.8 - - - -
211C GLU* 2.8 48.2 + - + +
289C ALA* 1.3 72.6 - - - +
291C TYR* 1.3 71.1 + - - +
292C GLY* 3.9 14.3 + - - -
340C ARG* 3.5 55.0 - - + +
342C PRO* 3.7 29.2 - - + -
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Residues in contact with TYR 291 (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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209C PHE 3.5 4.5 - - - -
210C LEU* 3.5 36.9 - - + +
224C PHE* 4.3 14.1 - + - -
283C ILE* 3.4 22.6 - - + +
289C ALA* 4.2 14.8 - - + +
290C PHE* 1.3 81.9 - - - +
292C GLY* 1.3 59.4 + - - +
342C PRO* 3.4 7.1 - - - +
343C MET* 3.0 41.6 + - + +
348C ILE* 3.7 45.8 - - + +
351C ILE* 4.5 8.3 - - + -
352C HIS* 2.7 30.6 + + - -
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Residues in contact with GLY 292 (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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208C ALA* 3.4 4.2 - - - +
209C PHE* 3.0 50.6 + - - +
290C PHE* 3.9 8.5 + - - -
291C TYR* 1.3 75.5 - - - +
293C VAL* 1.3 65.3 + - - +
341C SER 3.2 10.5 - - - -
343C MET* 4.0 4.8 - - - +
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Residues in contact with VAL 293 (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* 3.5 38.6 - - + -
207C SER 3.3 10.1 - - - +
208C ALA* 4.5 1.3 - - + -
209C PHE* 4.0 1.5 - - - -
292C GLY* 1.3 78.8 - - - +
294C THR* 1.3 67.7 + - - +
295C SER* 5.3 2.9 - - - +
321C LYS* 4.0 15.9 - - - +
338C ILE* 4.2 2.4 - - + +
340C ARG 3.7 0.5 + - - -
341C SER* 2.7 39.8 + - - +
343C MET* 3.8 21.3 - - + -
344C P1L 3.8 26.0 - - + -
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Residues in contact with THR 294 (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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205C GLU* 3.3 20.7 - - - +
206C PHE* 3.3 0.9 - - - -
207C SER* 2.8 45.2 + - - +
209C PHE* 3.5 13.8 - - - -
221C LYS* 5.8 0.6 + - - -
293C VAL* 1.3 71.5 + - - +
295C SER* 1.3 67.1 + - - +
338C ILE 3.4 8.5 - - - +
339C ASN* 3.8 13.3 + - - +
340C ARG* 3.1 22.5 + - - +
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Residues in contact with SER 295 (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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203C LEU* 4.2 2.5 - - - -
205C GLU* 3.3 12.3 - - - -
206C PHE* 3.8 21.2 - - - -
293C VAL* 5.3 2.3 - - - +
294C THR* 1.3 77.4 - - - +
296C GLN* 1.3 58.9 + - - +
297C TYR* 3.8 16.8 + - - -
323C GLU* 5.3 0.2 + - - -
336C TYR 3.8 0.4 - - - +
337C ARG* 3.6 2.3 - - - +
338C ILE* 2.8 64.7 + - - +
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Residues in contact with GLN 296 (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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203C LEU* 3.7 1.7 - - - +
204C VAL* 2.7 53.1 + - + +
205C GLU* 3.0 25.7 + - + +
294C THR* 6.3 0.2 - - + -
295C SER* 1.3 75.2 - - - +
297C TYR* 1.3 62.7 + - - +
298C GLU* 4.0 9.1 + - - -
333C ARG* 5.0 5.7 - - - +
335C VAL* 3.5 29.7 - - + +
336C TYR 3.2 5.8 - - - +
337C ARG* 3.2 35.6 + - + +
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Residues in contact with TYR 297 (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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201C LEU* 4.1 23.3 - - + -
202C ARG 3.2 7.4 - - - +
203C LEU* 3.3 40.9 - - + +
204C VAL* 4.9 0.2 - - - -
206C PHE* 5.6 0.2 - - - -
295C SER* 3.8 23.7 + - - -
296C GLN* 1.3 80.1 - - - +
298C GLU* 1.3 65.1 + - - +
305C VAL* 5.6 2.0 - - + -
307C CYS* 3.9 21.4 - - - +
325C GLU* 5.6 0.2 - - + -
335C VAL* 3.4 1.6 - - - -
336C TYR* 2.7 56.0 + - + -
338C ILE* 4.1 7.0 - - + +
374C LEU* 3.5 26.7 - - - +
376C VAL* 3.6 25.7 - - + +
386C LEU* 4.7 5.4 - - + -
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Residues in contact with GLU 298 (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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201C LEU* 3.6 2.9 - - - +
202C ARG* 2.9 39.3 + - + +
204C VAL* 3.4 30.4 - - + +
296C GLN* 4.0 10.4 + - - -
297C TYR* 1.3 75.6 - - - +
299C SER* 1.3 63.6 + - - +
333C ARG* 3.2 47.1 + - + +
334C PHE 3.0 12.3 - - - +
335C VAL* 4.3 3.1 - - + +
336C TYR* 3.9 2.9 - - - -
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Residues in contact with SER 299 (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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200C LYS 2.6 26.7 + - - -
201C LEU* 4.1 1.8 - - - -
298C GLU* 1.3 75.5 - - - +
300C SER* 1.3 61.1 + - - +
301C GLU* 2.6 27.0 + - - +
303C MET* 3.3 8.3 - - - +
333C ARG* 3.7 8.8 - - - -
334C PHE* 2.7 35.2 + - - +
336C TYR* 3.4 27.4 - - - -
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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