Contacts of the strand formed by residues 384 - 394 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A LEU* 3.7 27.1 + - + +
264A LYS* 5.1 3.7 - - - +
265A GLY* 4.7 16.3 + - - -
266A PRO* 3.7 21.9 - - - +
269A ALA* 4.4 2.2 - - + +
270A PHE* 4.0 27.4 - - + -
375A VAL* 4.5 8.6 - - + +
376A VAL 4.1 6.5 - - - +
377A THR* 4.4 5.4 + - - +
382A GLN 3.6 4.0 + - - -
383A GLU* 1.3 79.8 - - - +
385A LEU* 1.3 62.1 + - - +
386A LEU* 4.0 18.4 - - - +
387A CYS* 4.4 3.8 - - + -
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Residues in contact with LEU 385 (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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198A THR* 3.7 15.2 + - - +
200A LYS* 3.6 46.7 - - + +
201A LEU* 3.8 23.8 - - + +
266A PRO* 5.7 0.2 - - - +
269A ALA* 3.7 13.7 - - - +
303A MET* 4.2 10.5 - - + -
305A VAL* 3.6 30.3 - - + -
376A VAL* 2.8 13.5 + - + +
377A THR* 3.8 2.9 - - - -
378A ASN* 3.5 31.4 - - + +
383A GLU* 3.2 9.6 + - - +
384A THR* 1.3 74.8 - - - +
386A LEU* 1.3 65.9 + - - +
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Residues in contact with LEU 386 (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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196A ILE* 5.1 3.1 - - + -
197A GLY* 3.7 13.9 - - - +
201A LEU* 3.8 22.0 - - + +
203A LEU* 3.5 45.3 - - + +
269A ALA* 3.5 19.3 - - - +
271A PHE* 3.6 26.5 - - + -
297A TYR* 4.5 5.8 - - + -
374A LEU* 4.0 0.8 - - + +
375A VAL* 3.5 2.3 - - - +
376A VAL* 2.8 40.1 + - + +
384A THR* 3.6 2.4 - - - -
385A LEU* 1.3 82.0 - - - +
387A CYS* 1.3 65.6 + - - +
388A MET* 5.2 7.2 - - + +
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Residues in contact with CYS 387 (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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258A LEU* 4.0 7.4 - - - -
261A LEU* 5.2 2.0 - - + -
269A ALA 2.9 10.3 + - - +
270A PHE* 3.5 41.5 - - + -
271A PHE* 2.9 30.1 + - - +
373A LEU* 3.7 26.2 - - - -
374A LEU 3.3 2.7 - - - +
375A VAL* 3.9 16.2 - - + +
384A THR* 4.4 4.7 - - + -
386A LEU* 1.3 79.2 - - - +
388A MET* 1.3 64.9 + - - +
389A ALA 4.8 0.4 - - - -
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Residues in contact with MET 388 (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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196A ILE* 5.3 8.1 - - + -
203A LEU* 3.8 28.7 - - + -
206A PHE* 4.3 17.0 - - + -
227A ILE* 4.4 16.2 - - + -
271A PHE* 3.5 10.1 - - + +
273A VAL* 3.6 27.1 - - + -
275A PHE* 4.7 1.3 - - + -
373A LEU* 3.8 1.7 - - - -
374A LEU* 2.6 67.5 + - + +
386A LEU* 5.3 7.9 - - + -
387A CYS* 1.3 74.7 - - - +
389A ALA* 1.3 60.4 + - - +
390A CYS* 3.7 22.8 - - - -
405A ILE* 6.5 0.2 - - - -
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Residues in contact with ALA 389 (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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247A ILE* 4.1 9.6 - - + -
251A PHE* 3.4 27.6 - - + -
258A LEU* 4.4 9.0 - - + -
271A PHE 2.8 16.1 + - - +
272A LEU* 3.4 11.9 - - + +
273A VAL* 2.7 32.4 + - - -
372A ILE 3.8 4.0 - - - -
373A LEU* 3.9 12.3 - - + +
387A CYS 4.1 0.6 - - - -
388A MET* 1.3 71.0 - - - +
390A CYS* 1.3 57.5 + - - +
408A LEU* 4.5 0.4 - - + -
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Residues in contact with CYS 390 (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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206A PHE* 5.7 2.9 - - - -
251A PHE* 3.5 1.4 - - - -
273A VAL* 3.5 4.5 - - - -
275A PHE* 3.7 21.5 - - + -
371A THR* 3.4 12.5 - - - -
372A ILE* 2.8 44.7 + - + +
374A LEU* 5.1 1.6 - - - -
388A MET* 3.7 34.5 - - - -
389A ALA* 1.3 77.8 - - - +
391A VAL* 1.3 63.6 - - - +
392A PHE* 3.8 23.1 - - + -
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Residues in contact with VAL 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ILE* 6.2 0.9 - - + -
250A LYS* 5.8 1.8 - - + -
251A PHE* 4.3 7.2 - - + -
272A LEU* 4.1 17.9 - - + -
273A VAL 3.0 8.6 + - - +
274A LYS* 3.4 9.0 - - + +
275A PHE* 2.7 33.8 + - - +
367A LEU 5.9 1.6 - - - +
370A PHE 4.8 4.5 - - - +
371A THR* 4.1 15.7 - - + -
390A CYS* 1.3 80.3 - - - +
392A PHE* 1.3 67.4 + - - +
86B MET* 4.7 17.5 - - + -
95B PHE* 3.7 32.8 - - + -
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Residues in contact with PHE 392 (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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206A PHE* 6.5 0.2 - + - -
225A VAL* 4.5 2.7 - - + -
274A LYS* 4.3 2.7 - - - -
275A PHE* 3.3 39.0 - + + -
277A ALA* 4.8 3.4 - - + -
344A P1L 3.8 40.2 - - + -
364A ASN 5.1 0.2 - - - +
367A LEU* 3.4 36.5 + - + +
370A PHE* 3.5 37.0 + + - +
372A ILE* 3.5 25.4 - - + -
390A CYS* 3.8 31.4 - - + -
391A VAL* 1.3 81.3 - - - +
393A GLU* 1.3 70.0 + - - +
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Residues in contact with GLU 393 (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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274A LYS* 3.0 33.0 + - - +
275A PHE 2.8 8.8 + - - +
276A TRP* 3.5 26.0 + - + -
277A ALA* 2.8 28.0 + - - +
364A ASN* 3.5 35.1 + - + +
367A LEU* 3.9 4.6 - - - +
392A PHE* 1.3 78.2 - - - +
394A VAL* 1.3 65.2 + - - +
395A SER 4.0 0.2 - - - -
87B ARG* 3.4 27.2 + - - -
95B PHE 4.5 0.9 - - - +
96B PHE* 4.5 7.2 - - - +
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Residues in contact with VAL 394 (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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276A TRP* 4.3 6.2 - - - -
277A ALA* 3.5 11.4 - - + +
279A LEU* 3.7 39.5 - - + +
354A LEU* 5.3 0.2 - - + -
360A LYS* 4.1 25.7 - - + +
363A MET* 3.8 25.6 - - + -
364A ASN* 2.8 27.9 + - - +
367A LEU* 3.8 14.8 - - + -
393A GLU* 1.3 73.2 - - - +
395A SER* 1.3 73.2 - - - +
396A ASN* 3.4 4.5 + - - +
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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