Contacts of the strand formed by residues 224 - 232 (chain B) in PDB entry 1KWS
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 LEU 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A LYS 5.1 0.2 - - - +
316A MET* 3.7 9.1 - - - +
318A GLN* 3.6 8.3 - - + -
319A GLU* 3.3 34.5 - - - +
322A LEU* 3.3 35.9 - - + -
329A SER* 3.9 0.2 - - - +
220B LEU* 3.3 18.9 - - - -
221B VAL 3.1 9.0 + - - +
222B GLY 3.7 9.0 - - - +
223B GLY* 1.3 81.1 - - - +
225B ARG* 1.3 66.9 + - - +
226B PHE 3.0 14.9 + - - +
227B GLU* 4.7 5.6 - - + -
240B HIS* 3.8 17.0 - - + +
241B THR* 4.0 22.7 - - - -
242B ALA* 4.0 4.3 - - + +
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Residues in contact with ARG 225 (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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87A LEU* 4.9 12.1 - - + +
316A MET* 3.4 23.4 - - + +
319A GLU* 2.9 22.6 + - + +
329A SER* 3.8 18.2 + - - -
330A ASP 3.3 24.4 + - - -
331A PRO* 4.8 10.0 + - - -
333A ILE 3.0 22.0 + - - -
334A GLU* 4.3 1.4 - - - +
335A VAL* 3.5 35.5 + - + +
219B GLY* 3.4 1.9 - - - -
220B LEU* 2.7 29.1 + - + +
224B LEU* 1.3 71.6 - - - +
226B PHE* 1.3 68.5 + - - +
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Residues in contact with PHE 226 (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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329A SER* 3.5 18.1 + - - -
330A ASP* 3.6 41.5 - - + -
333A ILE* 3.8 24.0 - - + -
335A VAL* 4.1 2.9 - - + -
217B PRO* 3.9 22.7 - - + -
218B VAL 3.2 13.0 - - - +
219B GLY* 3.9 1.6 - - - -
220B LEU 4.1 0.2 - - - +
221B VAL 4.8 0.4 - - - +
224B LEU* 3.0 9.7 - - - +
225B ARG* 1.3 92.6 - - - +
227B GLU* 1.3 64.5 + - - +
228B GLY* 4.4 6.3 - - - -
240B HIS* 3.1 41.4 + + + -
301B CYS 5.4 4.3 - - - -
304B VAL* 3.8 18.6 - - + -
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Residues in contact with GLU 227 (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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216B TRP 4.6 0.5 - - - +
217B PRO* 3.3 0.9 - - - +
218B VAL* 2.8 31.9 + - + +
221B VAL* 3.8 33.2 - - + +
222B GLY* 4.2 15.2 - - - +
224B LEU* 4.7 3.9 - - + +
226B PHE* 1.3 76.8 - - - +
228B GLY* 1.3 58.4 + - - +
240B HIS 3.2 19.1 - - - +
241B THR* 2.8 27.4 + - - -
242B ALA 4.6 1.0 + - - -
243B TRP* 5.2 1.4 + - - +
247B ARG* 3.7 8.8 + - - -
250B PRO 3.8 17.2 - - - +
251B VAL* 4.3 1.4 - - - -
252B ASP* 3.9 17.0 + - - +
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Residues in contact with GLY 228 (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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216B TRP 4.9 0.2 - - - -
217B PRO* 3.9 11.7 - - - -
226B PHE* 4.1 6.2 - - - -
227B GLU* 1.3 77.1 - - - +
229B PRO* 1.3 72.8 - - - +
239B PHE* 4.6 4.0 - - - -
240B HIS* 2.7 46.8 + - - +
251B VAL* 5.9 2.2 - - - -
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Residues in contact with PRO 229 (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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215B VAL* 3.4 36.8 - - + -
216B TRP 4.0 14.1 - - - +
217B PRO 4.1 0.4 - - - -
228B GLY* 1.3 87.2 - - - +
230B GLN* 1.3 64.2 + - - +
231B VAL* 3.7 2.6 + - + -
236B VAL* 4.1 18.6 - - + -
238B GLY 3.5 6.5 - - - +
239B PHE* 4.0 15.7 - - + -
251B VAL* 4.7 5.6 - - + -
301B CYS* 3.8 36.9 - - + +
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Residues in contact with GLN 230 (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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229B PRO* 1.3 75.3 - - - +
231B VAL* 1.3 59.8 + - - +
236B VAL* 3.3 6.1 - - - -
237B VAL* 2.9 35.4 + - + -
238B GLY* 2.6 35.9 + - - +
239B PHE 3.6 10.0 + - - +
240B HIS* 3.9 29.5 + - - +
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Residues in contact with VAL 231 (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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229B PRO* 3.7 4.4 + - + +
230B GLN* 1.3 77.8 - - - +
232B GLN* 1.3 65.5 + - - +
233B ASP 4.7 0.2 - - - +
234B GLY* 3.6 16.2 - - - +
235B ARG 3.3 24.0 - - - +
236B VAL* 4.7 1.8 - - + -
237B VAL* 4.5 1.1 - - - -
296B PRO* 3.7 22.4 - - + -
300B ASN* 3.5 37.9 - - + +
301B CYS* 3.8 14.6 - - + -
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Residues in contact with GLN 232 (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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230B GLN 4.3 0.2 + - - -
231B VAL* 1.3 76.3 - - - +
233B ASP* 1.3 80.0 + - - +
234B GLY 3.1 0.2 - - - -
235B ARG* 2.9 25.1 + - - +
237B VAL* 3.7 26.2 - - + +
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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
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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