Contacts of the strand formed by residues 279 - 286 (chain A) in PDB entry 1KSW
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 GLY 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A NBS 5.7 1.1 - - - -
275A GLN* 3.6 5.5 + - - +
276A GLY* 3.0 29.9 + - - +
277A CYS 3.6 1.4 - - - -
278A PHE* 1.3 82.3 - - - +
280A GLU* 1.3 67.1 - - - +
295A LYS* 5.6 1.6 - - - -
296A THR 3.0 15.7 - - - -
297A LEU* 4.2 3.1 - - - +
298A LYS* 4.4 3.1 - - - -
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Residues in contact with GLU 280 (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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1A NBS 5.0 0.7 - - - -
272A LYS* 3.1 20.8 - - - -
274A GLY 3.7 9.2 - - - +
275A GLN* 3.0 36.8 + - + +
276A GLY 4.8 0.2 - - - +
279A GLY* 1.3 79.2 - - - -
281A VAL* 1.3 63.8 + - - +
282A TRP* 3.9 21.8 + - - +
295A LYS* 3.3 3.5 - - - +
296A THR* 2.6 49.1 + - - +
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Residues in contact with VAL 281 (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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1A NBS 3.2 76.1 - - + +
272A LYS* 3.8 0.7 - - - -
273A LEU* 2.7 37.6 + - + -
274A GLY 3.1 12.2 + - - +
280A GLU* 1.3 78.4 - - - +
282A TRP* 1.3 65.7 + - - +
293A ALA* 5.3 0.2 - - + -
294A ILE 3.2 4.9 - - - +
295A LYS* 3.7 31.0 - - + -
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Residues in contact with TRP 282 (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 LEU* 3.9 36.8 - - + +
270A GLU 3.6 20.6 - - - -
271A VAL 3.1 30.5 - - - -
272A LYS* 3.3 42.4 - - + +
273A LEU* 3.9 4.7 - - - -
280A GLU* 3.9 26.6 + - + +
281A VAL* 1.3 87.6 - - - +
283A MET* 1.3 62.3 + - - +
284A GLY 3.8 0.2 + - - -
293A ALA* 3.5 3.8 - - - +
294A ILE* 2.7 44.6 + - + +
296A THR* 4.6 12.2 + - + +
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Residues in contact with MET 283 (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 LEU 4.1 0.2 - - - -
270A GLU* 3.0 49.4 + - + +
271A VAL* 2.8 39.3 + - + +
273A LEU* 3.6 22.9 - - + +
282A TRP* 1.3 74.0 - - - +
284A GLY* 1.3 58.6 + - - +
291A ARG* 3.2 43.1 - - - +
292A VAL 3.6 6.3 - - - +
293A ALA* 4.6 1.1 - - - +
340A TYR* 4.1 19.5 - - + -
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Residues in contact with GLY 284 (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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268A ARG 3.2 13.0 - - - -
270A GLU* 4.0 6.1 - - - -
282A TRP 3.8 1.0 + - - -
283A MET* 1.3 78.4 - - - +
285A THR* 1.3 65.9 + - - -
290A THR 3.2 2.3 - - - +
291A ARG* 3.7 7.0 + - - -
292A VAL* 2.7 42.2 + - - -
294A ILE* 3.9 9.3 - - - +
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Residues in contact with THR 285 (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 LEU* 3.3 2.4 - - - -
268A ARG* 2.6 55.5 + - - +
270A GLU* 3.0 22.1 + - - -
284A GLY* 1.3 77.6 + - - -
286A TRP* 1.3 53.7 + - - +
288A GLY* 3.3 12.3 - - - -
289A THR 3.0 34.5 - - - +
290A THR 3.0 14.8 + - - +
291A ARG* 3.5 7.1 + - - -
292A VAL* 3.9 3.1 - - - +
294A ILE* 4.7 0.4 - - - +
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Residues in contact with TRP 286 (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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95A ARG* 4.3 15.0 - - + -
96A THR* 4.1 20.6 - - + -
255A LEU* 3.3 53.2 - - + -
256A ALA* 4.2 6.7 - - + -
259A ALA* 4.9 3.8 - - + -
262A ILE* 3.6 30.2 - - + +
263A PRO* 6.2 0.9 - - + -
266A SER* 2.7 49.4 + - - -
267A LEU* 3.6 11.9 - - + -
285A THR* 1.3 72.9 - - - +
287A ASN* 1.3 90.0 + - + +
288A GLY 3.3 0.7 + - - -
289A THR* 3.4 0.3 + - - -
290A THR* 3.3 37.1 + - - -
292A VAL* 3.8 15.1 - - + +
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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