Contacts of the strand formed by residues 288 - 296 (chain A) in PDB entry 1KTW
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 VAL 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A MET* 4.1 14.4 - - - -
259A ILE* 4.5 2.2 - - + -
262A ILE* 3.4 29.4 - - + +
263A PHE 5.9 0.2 - - - -
264A ALA* 5.9 0.7 - - + -
278A PHE* 4.0 21.1 - - + -
286A GLY 4.1 0.8 + - - +
287A ASP* 1.3 80.2 - - - +
289A GLN* 1.3 64.0 + - - +
290A VAL* 4.0 22.0 - - + -
375A PHE* 4.1 29.8 - - + -
377A THR 3.0 8.5 + - - +
378A VAL* 3.4 7.3 - - + +
379A LYS 3.3 23.1 + - - +
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Residues in contact with GLN 289 (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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30A PRO* 3.6 17.9 - - + +
31A LYS* 3.0 62.7 + - - +
33A TYR* 4.7 6.1 - - - -
262A ILE 3.0 7.7 + - - -
263A PHE* 3.5 32.2 - - + +
264A ALA 3.0 25.8 + - - +
288A VAL* 1.3 73.7 - - - +
290A VAL* 1.3 71.4 + - - +
291A THR* 4.5 5.3 - - - +
379A LYS* 3.6 10.3 - - + +
381A PHE* 4.5 10.6 - - + -
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Residues in contact with VAL 290 (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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242A LEU* 5.3 0.2 - - + -
244A MET* 4.9 2.5 - - + -
264A ALA* 3.4 22.9 - - + +
267A ILE* 4.7 3.4 - - + -
276A VAL* 4.2 20.6 - - + -
278A PHE* 4.5 15.0 - - + -
288A VAL* 4.0 17.9 - - + -
289A GLN* 1.3 79.9 - - - +
291A THR* 1.3 71.5 - - - +
293A VAL* 3.6 28.5 - - + -
378A VAL* 5.9 0.2 - - + -
379A LYS 3.0 7.5 + - - +
380A VAL* 3.3 14.7 - - + -
381A PHE* 2.9 26.3 + - - -
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Residues in contact with THR 291 (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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30A PRO* 3.7 35.0 - - + -
33A TYR* 5.1 2.8 + - - -
264A ALA 3.0 6.3 + - - -
265A ASP* 2.7 32.9 + - - +
266A ASN 3.0 23.0 + - - -
289A GLN* 4.5 8.3 - - - +
290A VAL* 1.3 83.4 - - - +
292A ASN* 1.3 69.9 + - - +
293A VAL* 3.8 0.8 - - - +
381A PHE* 3.4 16.2 - - + -
382A ASP* 5.3 1.8 - - - +
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Residues in contact with ASN 292 (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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265A ASP* 2.9 22.7 + - - +
266A ASN* 3.1 33.8 - - + +
267A ILE 3.3 3.6 + - - +
291A THR* 1.3 75.9 - - - +
293A VAL* 1.3 58.2 + - - +
294A SER* 4.2 1.7 + - - -
381A PHE 2.8 13.7 + - - -
382A ASP* 3.3 26.8 + - - +
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Residues in contact with VAL 293 (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 ILE* 3.5 7.0 - - + +
275A ALA* 3.6 26.7 - - + -
276A VAL* 4.0 12.6 - - + -
290A VAL* 3.6 31.4 - - + -
292A ASN* 1.3 75.6 - - - +
294A SER* 1.3 64.9 + - - +
301A ALA* 3.8 16.4 - - + +
302A VAL* 4.3 6.5 - - + -
380A VAL* 3.9 18.8 - - + -
382A ASP 2.9 8.8 + - - +
383A VAL* 3.4 10.4 - - + -
384A THR* 3.0 24.3 + - - -
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Residues in contact with SER 294 (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 ASN* 5.2 0.7 + - - -
267A ILE 3.1 5.9 + - - +
268A ARG* 3.2 34.6 - - - +
269A CYS 3.2 20.4 + - - -
275A ALA* 3.8 5.1 - - - +
292A ASN 4.2 1.0 + - - -
293A VAL* 1.3 76.5 - - - +
295A SER* 1.3 63.4 + - - +
296A VAL* 6.4 0.7 - - - -
301A ALA* 4.8 1.3 - - - -
384A THR* 3.2 18.8 - - - -
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Residues in contact with SER 295 (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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269A CYS* 3.3 15.7 - - - -
294A SER* 1.3 76.2 - - - +
296A VAL* 1.3 69.1 + - - +
297A SER 4.3 0.2 - - - -
298A CYS* 4.0 21.7 + - - +
300A SER 4.2 1.9 - - - -
301A ALA* 3.6 29.1 + - - +
384A THR* 3.0 5.6 + - - +
385A ALA* 3.6 13.9 - - - +
386A ARG* 2.9 26.5 + - - +
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Residues in contact with VAL 296 (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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269A CYS 3.1 9.3 + - - +
270A SER* 3.2 12.4 - - - -
271A LYS* 3.1 18.0 + - - +
294A SER* 6.4 0.4 - - - -
295A SER* 1.3 80.9 - - - +
297A SER* 1.3 73.5 + - - +
298A CYS 3.4 0.2 - - - -
386A ARG* 3.5 35.0 - - + +
387A PHE 4.8 3.4 - - - +
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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