Contacts of the strand formed by residues 288 - 296 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LYS* 6.3 0.2 - - - -
244B MET* 4.1 9.0 - - - -
259B ILE* 4.6 5.2 - - + -
262B ILE* 3.3 32.3 - - + +
263B PHE 5.9 0.4 - - - -
264B ALA* 6.0 0.7 - - + -
278B PHE* 4.1 18.4 - - + -
286B GLY 4.0 2.0 + - - +
287B ASP* 1.3 80.4 - - - +
289B GLN* 1.3 62.8 + - - +
290B VAL* 4.1 20.6 - - + -
375B PHE* 4.1 31.2 - - + -
377B THR 3.1 8.5 + - - +
378B VAL* 3.3 10.1 - - + +
379B LYS 3.2 22.9 + - - +
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Residues in contact with GLN 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PRO* 3.5 16.3 - - - +
31B LYS* 2.8 63.9 + - - +
33B TYR* 4.7 5.9 - - - -
262B ILE 3.0 7.5 + - - +
263B PHE* 3.5 34.1 - - + -
264B ALA 3.0 24.4 + - - +
288B VAL* 1.3 73.5 - - - +
290B VAL* 1.3 68.7 + - - +
291B THR* 4.2 9.6 - - + +
379B LYS* 3.5 10.3 - - + +
381B PHE* 4.3 11.2 - - + -
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Residues in contact with VAL 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 5.3 0.2 - - + -
244B MET* 4.9 2.7 - - + -
264B ALA* 3.4 22.2 - - + +
267B ILE* 4.7 2.9 - - + -
276B VAL* 4.2 25.1 - - + -
278B PHE* 4.5 3.1 - - + -
288B VAL* 4.1 17.5 - - + -
289B GLN* 1.3 79.0 - - - +
291B THR* 1.3 71.5 + - - +
293B VAL* 3.4 29.6 - - + -
378B VAL* 5.9 0.2 - - + -
379B LYS 2.9 7.6 + - - +
380B VAL* 3.2 21.3 - - + -
381B PHE* 2.9 25.3 + - - -
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Residues in contact with THR 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PRO* 3.8 33.0 - - + -
33B TYR* 5.2 2.4 + - + -
264B ALA 3.0 7.2 + - - +
265B ASP* 2.6 34.2 + - - +
266B ASN 3.0 15.6 + - - -
289B GLN* 4.2 11.2 - - + +
290B VAL* 1.3 84.8 - - - +
292B ASN* 1.3 75.2 + - - +
293B VAL* 3.8 0.7 - - - -
381B PHE* 3.4 14.8 - - + -
382B ASP* 5.5 1.8 - - - -
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Residues in contact with ASN 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B ASP* 2.9 20.3 - - - +
266B ASN* 3.1 30.2 - - + +
267B ILE 3.3 4.2 + - - +
291B THR* 1.3 78.0 + - - +
293B VAL* 1.3 60.1 + - - +
294B SER* 5.3 0.9 + - - -
381B PHE 2.9 13.9 + - - -
382B ASP* 3.4 28.6 + - - +
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ILE* 3.5 7.2 - - + +
275B ALA* 3.8 24.7 - - + -
276B VAL* 4.0 11.7 - - + -
290B VAL* 3.4 32.5 - - + -
291B THR 4.5 1.1 - - - +
292B ASN* 1.3 74.4 - - - +
294B SER* 1.3 65.7 + - - +
301B ALA* 3.8 17.5 - - + +
302B VAL* 4.1 9.9 - - + -
380B VAL* 4.0 15.3 - - + -
382B ASP 3.0 9.9 + - - +
383B VAL* 3.3 9.9 - - + +
384B THR* 3.0 24.4 + - - -
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Residues in contact with SER 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B ASN* 5.1 4.9 + - - -
267B ILE 3.2 7.2 + - - +
268B ARG* 3.3 34.2 + - - +
269B CYS 3.2 19.9 + - - -
275B ALA* 3.8 5.2 - - - +
292B ASN 5.3 1.2 + - - -
293B VAL* 1.3 78.3 - - - +
295B SER* 1.3 63.4 + - - +
301B ALA* 4.9 0.4 - - - -
384B THR* 3.2 19.7 - - - -
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Residues in contact with SER 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B ARG* 4.9 0.9 - - - +
269B CYS* 3.3 14.6 - - - -
294B SER* 1.3 77.4 - - - +
296B VAL* 1.3 70.1 + - - +
298B CYS* 4.0 21.1 + - - +
300B SER* 4.3 1.4 - - - -
301B ALA* 3.6 21.7 + - - +
384B THR* 3.0 8.7 + - - +
385B ALA* 3.6 22.0 - - - +
386B ARG* 3.0 24.6 + - - +
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ARG* 2.9 35.0 - - - +
269B CYS 3.1 9.1 + - - +
270B SER* 3.2 10.3 - - - -
271B LYS* 3.1 16.1 + - - +
295B SER* 1.3 78.7 - - - +
297B SER* 1.3 78.0 + - - +
386B ARG* 3.5 36.1 - - + +
387B PHE 5.0 2.7 - - - +
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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