Contacts of the strand formed by residues 353 - 369 (chain A) in PDB entry 3KVA
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 ILE 353 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A PHE* 4.0 22.9 - - + -
282A HIS 3.6 7.9 - - - +
283A ILE* 3.8 19.1 - - + -
302A TYR 3.6 0.2 - - - +
303A LEU* 3.6 0.9 - - - +
304A ILE* 2.7 59.7 + - + +
305A LYS 4.8 1.8 - - - +
306A PRO* 5.0 0.4 - - + -
310A ASN* 3.6 30.3 - - + +
311A LEU* 4.4 9.6 - - + -
314A TYR* 3.7 21.5 - - + -
328A PHE* 4.0 19.1 - - + -
351A GLY 3.9 4.7 - - - +
352A TRP* 1.3 73.5 - - - +
354A HIS* 1.3 62.4 + - - +
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Residues in contact with HIS 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE* 3.2 6.6 - - - -
282A HIS* 3.0 46.1 + + - -
284A ASP* 3.3 17.0 + - - -
290A VAL* 5.1 1.8 - - - +
301A PHE* 4.0 24.4 - + + -
302A TYR 2.9 13.9 - - - +
303A LEU* 3.7 19.3 - - + -
348A VAL* 4.8 11.4 - - + +
352A TRP 3.0 18.5 + - - -
353A ILE* 1.3 76.7 - - - +
355A ALA* 1.3 61.2 + - - +
356A VAL* 4.2 3.6 - - + -
489A FE2 2.5 30.6 - - - -
701A AKG 3.3 15.2 + - - -
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Residues in contact with ALA 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TYR* 3.7 18.4 - - + +
279A THR* 3.3 16.8 - - - +
280A ASP 4.3 0.2 - - - -
281A PHE* 3.6 33.2 - - + +
282A HIS* 5.2 0.4 - - - -
301A PHE* 3.4 0.9 - - - +
302A TYR* 2.8 36.7 + - + -
354A HIS* 1.3 73.8 - - - +
356A VAL* 1.3 67.9 + - - +
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Residues in contact with VAL 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A SER 3.7 0.9 - - - +
278A TYR* 3.4 8.9 - - - -
279A THR* 2.9 32.4 + - - -
282A HIS* 5.5 0.4 - - + -
299A LYS* 3.6 32.1 - - + -
300A ILE 3.4 5.2 - - - +
301A PHE* 3.6 41.1 - - + -
302A TYR* 4.8 0.4 - - - -
354A HIS* 4.2 7.9 - - + -
355A ALA* 1.3 81.5 - - - +
357A LEU* 1.3 64.5 - - - +
358A THR* 4.3 0.4 - - - +
701A AKG 3.7 37.2 + - + +
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Residues in contact with LEU 357 (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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123A ILE* 4.5 13.7 - - + -
126A LEU* 4.0 17.9 - - + -
127A ARG* 4.2 28.7 - - + +
276A ASP* 3.9 24.2 - - - +
277A SER 3.4 10.8 - - - +
278A TYR* 4.5 2.7 - - + -
299A LYS* 3.5 1.7 - - - -
300A ILE* 2.8 49.5 + - + +
302A TYR* 3.6 31.4 - - + +
356A VAL* 1.3 77.6 - - - +
358A THR* 1.3 71.8 + - - +
359A SER* 3.2 4.8 + - - +
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Residues in contact with THR 358 (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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224A ASN* 4.5 0.2 + - - -
273A GLY* 3.8 12.1 - - - +
274A VAL 3.2 27.6 - - - +
276A ASP* 2.6 32.6 + - - -
277A SER* 2.9 25.8 + - - -
298A GLU 3.7 4.3 - - - -
299A LYS* 3.4 24.4 + - - +
357A LEU* 1.3 72.7 - - - +
359A SER* 1.3 57.3 + - - +
360A GLN 3.0 27.0 + - - +
362A CYS* 4.0 11.0 - - + -
701A AKG 5.0 2.4 + - - -
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Residues in contact with SER 359 (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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127A ARG* 3.1 32.0 + - - +
275A GLN* 3.2 13.0 + - - +
298A GLU* 3.0 45.2 + - - +
300A ILE* 3.8 26.9 - - - -
357A LEU* 3.2 5.6 + - - -
358A THR* 1.3 72.9 - - - +
360A GLN* 1.3 64.6 + - - +
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Residues in contact with GLN 360 (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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275A GLN* 4.0 16.2 - - - +
297A GLY* 3.7 18.7 + - - -
298A GLU* 3.4 33.8 + - + +
358A THR* 3.0 15.5 - - - +
359A SER* 1.3 88.2 + - - +
361A ASP* 1.3 69.6 + - - +
362A CYS* 2.9 9.7 + - - +
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Residues in contact with ASP 361 (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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214A PHE* 4.1 16.2 - - + -
219A ARG* 2.6 43.2 + - - -
273A GLY 3.6 6.1 - - - -
274A VAL* 3.4 2.3 - - - -
275A GLN* 3.0 27.9 + - - +
296A TRP* 3.2 14.6 - - + -
297A GLY* 3.2 17.0 - - - -
360A GLN* 1.3 70.0 - - - +
362A CYS* 1.3 58.9 + - - +
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Residues in contact with CYS 362 (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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214A PHE* 4.7 1.2 - - - -
271A LEU 4.4 0.4 - - - -
272A MET* 3.4 5.5 - - - +
273A GLY 3.1 30.9 + - - +
294A VAL* 3.9 7.6 - - - -
296A TRP* 3.3 24.7 - - - +
298A GLU 3.7 11.2 - - - +
299A LYS* 3.8 34.3 - - - -
358A THR* 4.0 10.8 - - + -
360A GLN 2.9 13.8 + - - +
361A ASP* 1.3 73.2 - - - +
363A MET* 1.3 81.7 + - - +
364A ALA* 4.2 1.8 - - - -
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Residues in contact with MET 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PHE* 3.8 30.1 - - - +
178A SER 3.5 19.3 - - - +
179A VAL* 3.7 9.2 - - + +
182A VAL* 3.3 28.7 - - + -
270A CYS* 4.3 4.7 - - - -
271A LEU 3.1 11.0 - - - +
272A MET* 4.1 12.8 - - + -
295A LEU* 2.9 32.8 + - + +
296A TRP* 3.2 34.1 + - + +
362A CYS* 1.3 76.6 - - - +
364A ALA* 1.3 65.3 + - - +
365A PHE* 4.1 16.6 - - + -
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Residues in contact with ALA 364 (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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270A CYS* 3.6 1.7 - - - -
271A LEU* 2.7 39.9 + - + +
292A TYR* 4.2 26.5 - - + -
293A HIS 3.0 21.8 - - - +
294A VAL* 3.9 5.2 - - - -
295A LEU 4.1 1.6 - - - +
299A LYS* 4.5 0.9 - - - -
362A CYS* 4.2 9.8 - - - -
363A MET* 1.3 76.2 - - - +
365A PHE* 1.3 67.2 + - - +
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Residues in contact with PHE 365 (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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172A LEU* 4.0 23.8 - - + -
173A PRO* 4.3 19.7 - - + -
177A PHE* 4.6 4.9 - + - -
230A PHE* 3.8 25.8 - + + -
235A MET* 4.8 6.5 - - + -
239A VAL* 4.5 11.0 - - + -
269A TYR 3.2 15.3 - - - +
270A CYS* 3.9 17.3 - - - -
271A LEU* 4.0 4.9 - - - -
291A TRP* 3.5 18.2 - - + -
292A TYR* 3.5 3.6 - - - -
293A HIS* 2.8 34.0 + - + +
295A LEU* 4.1 30.3 - - + -
363A MET* 4.1 19.5 - - - -
364A ALA* 1.3 80.1 - - - +
366A GLY* 1.3 58.7 + - - +
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Residues in contact with GLY 366 (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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267A GLN 3.3 6.6 - - - +
268A LYS* 3.6 0.3 - - - -
269A TYR* 3.0 35.2 + - - -
271A LEU* 4.1 6.7 - - - +
290A VAL* 5.3 0.2 - - - -
291A TRP* 3.1 28.8 - - - -
292A TYR* 4.4 4.3 - - - -
365A PHE* 1.3 77.4 - - - +
367A GLY* 1.3 58.0 + - - -
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Residues in contact with GLY 367 (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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266A VAL 3.7 4.3 - - - -
267A GLN* 3.6 11.0 - - - -
269A TYR* 4.3 2.9 - - - -
290A VAL* 3.1 9.1 - - - +
291A TRP* 3.1 47.2 + - - +
366A GLY* 1.3 74.8 - - - -
368A ASN* 1.3 69.7 + - - -
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Residues in contact with ASN 368 (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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266A VAL* 2.8 28.3 + - + +
267A GLN* 4.6 9.0 + - - +
269A TYR* 3.7 10.2 - - - -
284A ASP* 3.7 23.4 + - - -
285A PHE* 3.5 32.9 - - + -
288A THR* 2.9 26.9 + - + +
289A SER 3.3 6.2 + - - -
290A VAL* 4.2 5.1 - - - +
367A GLY* 1.3 81.8 + - - -
369A PHE* 1.3 66.7 + - - +
396A PHE* 6.1 0.2 - - - -
491A OXY 3.5 18.1 + - - -
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Residues in contact with PHE 369 (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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156A PHE* 4.3 12.3 - + - -
244A ILE* 5.6 1.3 - - + -
245A ALA* 3.9 33.4 - - + +
248A LEU* 4.0 30.5 - - + -
249A SER* 4.0 21.3 - - - -
267A GLN* 6.3 0.4 - - + -
288A THR* 3.9 3.2 - - - -
289A SER* 3.0 55.0 + - - -
290A VAL 4.2 16.4 - - - -
291A TRP* 4.4 12.1 - + + -
347A PHE* 4.9 9.0 - + - -
368A ASN* 1.3 79.7 - - - +
370A LEU* 1.3 65.2 + - - +
371A HIS* 3.7 23.3 + + - -
378A GLN* 4.6 0.2 - - - +
396A PHE* 5.9 0.7 - - - -
490A FE2 3.8 5.2 - - - -
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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
------------------------------------------------------------
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