Contacts of the strand formed by residues 292 - 300 (chain C) in PDB entry 1KYZ
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 LYS 292 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C TYR* 3.9 6.5 - - - -
197C GLY* 3.1 27.5 + - - -
200C GLY* 5.8 3.3 - - - +
260C ASP 4.0 1.4 + - - +
261C ALA* 3.4 14.9 - - + +
262C VAL 3.0 21.7 + - - +
287C LEU* 3.3 16.2 - - - +
290C ASN 4.9 1.8 - - - +
291C GLY* 1.3 76.4 - - - +
293C VAL* 1.3 61.5 + - - +
294C ILE* 3.9 16.2 - - + -
360C GLU* 3.0 38.5 + - + +
361C PHE 3.1 14.8 - - - +
362C LEU* 4.1 13.2 - - + -
363C LYS 4.4 0.2 - - - +
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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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262C VAL* 3.3 22.2 - - + +
264C MET* 3.8 31.0 - - + -
280C LEU* 4.9 2.2 - - + -
283C CYS* 3.8 15.9 - - + -
287C LEU* 3.8 7.4 - - + -
292C LYS* 1.3 74.4 - - - +
294C ILE* 1.3 64.6 + - - +
295C VAL* 3.6 8.9 + - + +
344C PHE* 3.4 34.5 - - + -
360C GLU* 3.6 2.8 - - - +
361C PHE* 2.8 43.7 + - + +
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Residues in contact with ILE 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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195C TYR* 3.6 35.4 - - + +
197C GLY 4.9 0.2 - - - +
198C PHE* 3.7 32.5 - - + -
204C LEU* 4.8 2.5 - - + -
261C ALA* 4.6 11.0 - - + -
262C VAL 2.6 15.2 + - - +
263C PHE* 3.4 30.9 - - + -
264C MET 3.3 23.0 + - - -
292C LYS* 3.9 24.5 - - + +
293C VAL* 1.3 72.2 - - - +
295C VAL* 1.3 60.3 + - - +
296C ALA 4.0 0.2 + - - -
358C ILE* 3.7 16.4 - - + -
359C MET 3.6 3.1 - - - +
360C GLU* 4.8 1.8 - - + +
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Residues in contact with VAL 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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264C MET* 3.6 31.4 - - + +
265C LYS 4.8 4.3 - - - +
268C CYS* 4.4 7.6 - - - -
293C VAL* 3.9 10.3 - - + +
294C ILE* 1.3 74.3 - - - +
296C ALA* 1.3 62.5 + - - +
297C GLU* 3.6 25.5 + - + -
335C PHE* 4.7 2.5 - - + -
357C TYR 3.4 0.9 - - - +
358C ILE* 3.2 4.0 - - - -
359C MET* 2.6 55.4 + - + +
361C PHE* 3.7 35.0 - - + -
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Residues in contact with ALA 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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191C ILE* 4.5 2.0 - - + -
263C PHE* 4.3 7.2 - - + -
265C LYS* 3.1 32.9 - - + +
266C TRP* 3.0 28.6 + - - -
294C ILE 4.0 0.4 + - - -
295C VAL* 1.3 72.7 - - - +
297C GLU* 1.3 61.0 + - - +
356C THR* 4.1 12.8 - - + -
357C TYR 3.3 6.5 - - - -
358C ILE* 3.3 22.9 - - + -
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Residues in contact with GLU 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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266C TRP* 3.3 18.0 - - - -
267C ILE 3.2 7.3 + - - -
268C CYS* 3.1 14.7 + - + -
269C HIS* 2.9 50.7 + - + -
295C VAL* 3.6 20.8 - - + -
296C ALA* 1.3 82.3 - - - +
298C CYS* 1.3 64.4 + - - +
299C ILE* 3.6 2.8 + - - +
335C PHE* 3.5 26.9 - - + -
356C THR* 4.0 5.8 - - - +
357C TYR* 3.0 30.9 + - - +
359C MET* 3.7 6.9 - - + +
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Residues in contact with CYS 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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266C TRP* 5.4 4.8 - - - -
269C HIS* 5.5 0.6 + - - +
297C GLU* 1.3 77.8 + - - +
299C ILE* 1.3 61.8 + - - +
300C LEU 3.9 0.2 + - - -
312C GLY 5.6 0.9 - - - -
313C VAL* 3.7 28.6 - - + +
316C ILE* 5.4 8.5 - - + -
329C GLU* 3.9 17.7 + - - +
330C ARG 3.8 4.9 + - - +
335C PHE* 3.8 13.3 - - - -
354C PHE 5.4 0.2 - - - -
355C ASN* 3.7 38.8 - - - +
356C THR* 4.2 10.1 - - - -
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Residues in contact with ILE 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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297C GLU 3.6 2.7 + - - +
298C CYS* 1.3 75.1 - - - +
300C LEU* 1.3 64.6 + - - +
301C PRO* 3.8 7.0 - - + +
313C VAL* 4.0 9.8 - - - +
330C ARG 3.6 2.2 - - - -
331C THR 3.8 1.1 - - - -
332C GLN* 3.3 42.0 - - + +
335C PHE* 4.6 0.9 - - + -
349C VAL* 4.0 18.4 - - + -
355C ASN* 4.4 4.8 + - - -
357C TYR* 3.5 58.9 - - + -
359C MET* 4.2 23.3 - - + -
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Residues in contact with LEU 300 (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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298C CYS 3.9 0.4 + - - -
299C ILE* 1.3 75.9 - - - +
301C PRO* 1.3 76.1 - - + +
313C VAL* 3.6 31.6 - - + -
314C VAL* 4.1 18.2 - - + +
317C ASP* 4.6 10.3 - - + +
329C GLU* 3.3 33.2 - - + +
330C ARG* 2.7 24.3 + - - +
331C THR* 2.9 27.8 + - - +
334C GLU* 5.3 2.0 - - - +
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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