Contacts of the strand formed by residues 253 - 264 (chain B) in PDB entry 3K2H
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 ALA 253 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373A ARG* 4.9 0.4 - - - +
243B VAL 3.4 0.7 - - - +
244B LEU* 3.6 7.6 - - - -
245B LYS* 2.9 30.3 + - - +
247B ASN* 3.7 9.5 - - - +
252B ASP* 1.3 75.6 - - - +
254B TYR* 1.3 62.0 + - - +
255B SER* 3.6 3.9 + - - -
454B HIS* 3.8 21.1 - - + -
455B ILE 3.4 21.5 - - - +
456B TYR* 3.7 14.8 - - + +
457B VAL 4.3 0.4 - - - +
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Residues in contact with TYR 254 (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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238B VAL* 3.2 26.5 - - + +
239B LEU* 5.3 9.6 - - + -
242B GLY 3.9 12.3 - - - -
243B VAL 3.4 2.5 - - - -
244B LEU* 3.8 46.2 - - + +
253B ALA* 1.3 70.5 - - - +
255B SER* 1.3 60.1 + - - +
454B HIS* 2.9 3.5 - - - -
455B ILE* 2.8 48.6 + - + +
457B VAL* 4.1 10.3 - - + +
460B VAL* 4.0 25.6 - - + -
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Residues in contact with SER 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A TYR* 2.6 31.4 + - - -
238B VAL* 4.2 0.7 - - - -
242B GLY* 3.2 4.3 - - - -
243B VAL* 2.8 36.3 + - - +
245B LYS* 3.6 13.7 - - - -
253B ALA 4.2 4.3 - - - -
254B TYR* 1.3 74.5 - - - +
256B LYS* 1.3 60.7 + - - +
452B ASP* 3.0 25.7 + - - -
453B ALA 3.2 4.7 - - - -
454B HIS* 3.9 6.3 - - - -
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Residues in contact with LYS 256 (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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262A ARG* 5.5 5.3 - - - +
400A TYR* 3.7 8.5 - - - -
237B ASP* 3.0 24.9 + - - +
238B VAL* 4.3 8.0 - - + +
241B HIS* 4.1 35.7 - - + +
242B GLY* 4.3 2.5 - - - +
255B SER* 1.3 74.3 + - - +
257B PHE* 1.3 66.4 + - - +
258B GLY 5.9 0.2 + - - -
259B TYR* 3.5 28.4 + - + +
451B ALA 3.4 0.5 - - - +
452B ASP* 3.8 0.5 - - - -
453B ALA* 2.7 36.1 + - - +
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Residues in contact with PHE 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ARG* 2.8 23.4 + - - -
398A GLN* 3.8 17.0 - - - -
399A PHE 4.6 0.4 - - - -
400A TYR* 3.4 51.8 - + + -
407A SER* 3.8 22.0 - - - +
408A CYS* 3.8 8.1 - - - -
409A MET* 3.5 45.1 - - + -
445A GLU* 4.5 3.2 - - - +
447A VAL* 4.2 13.2 - - + -
256B LYS* 1.3 83.5 + - - +
258B GLY* 1.3 62.3 + - - +
259B TYR* 4.6 1.9 - - - -
451B ALA* 3.2 35.4 - - + -
452B ASP 4.3 0.4 - - - -
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Residues in contact with GLY 258 (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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260A GLN* 4.0 1.6 - - - -
262A ARG* 2.8 28.4 + - - -
409A MET* 3.4 18.4 - - - -
447A VAL* 4.5 1.8 - - - -
256B LYS* 4.1 0.9 + - - -
257B PHE* 1.3 76.5 - - - +
259B TYR* 1.3 75.3 + - - +
450B LEU 3.2 7.6 - - - -
451B ALA 2.9 14.1 + - - -
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Residues in contact with TYR 259 (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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260A GLN* 3.1 17.8 + - - +
234B ILE* 3.6 48.9 - - + -
237B ASP* 2.5 34.2 + - + -
238B VAL* 3.8 7.0 - - + +
256B LYS* 3.5 40.5 - - + +
257B PHE 4.5 0.7 - - - -
258B GLY* 1.3 83.6 - - - -
260B GLN* 1.3 60.9 + - - +
448B HIS 4.4 0.2 - - - -
449B ASN* 3.4 1.4 - - - -
450B LEU* 2.9 36.9 + - + +
453B ALA* 3.9 31.0 - - + -
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Residues in contact with GLN 260 (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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259A TYR* 3.1 43.9 + - - -
260A GLN* 3.4 22.6 + - + +
449A ASN* 4.7 1.8 + - - -
230B GLN* 4.5 2.9 - - - +
234B ILE* 5.2 0.9 - - - +
259B TYR* 1.3 76.5 - - - +
261B MET* 1.3 67.4 + - - +
262B ARG* 3.9 11.9 + - - +
409B MET* 3.8 7.9 - - - +
447B VAL* 3.7 22.7 - - + +
448B HIS 3.3 3.6 - - - -
449B ASN* 2.9 27.1 + - - +
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Residues in contact with MET 261 (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* 3.3 17.5 - - + +
231B TYR* 4.0 26.2 - - + -
234B ILE* 3.7 28.0 - - + -
260B GLN* 1.3 77.0 - - - +
262B ARG* 1.3 65.2 + - - +
263B PHE* 3.8 22.9 - - + -
421B VAL* 4.2 8.1 - - + -
425B ILE* 4.0 15.3 - - + -
447B VAL* 3.4 4.0 - - - +
448B HIS* 2.8 63.7 + - + +
450B LEU* 4.2 17.9 - - + -
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Residues in contact with ARG 262 (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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256A LYS* 5.5 6.0 - - - +
257A PHE 2.8 24.9 + - - -
258A GLY* 2.6 28.7 + - - -
259A TYR* 4.8 0.4 - - - +
227B GLU* 4.0 6.1 - - - +
230B GLN* 2.8 34.2 + - - +
260B GLN* 3.9 13.0 + - - -
261B MET* 1.3 76.7 - - - +
263B PHE* 1.3 65.4 + - - +
445B GLU* 2.8 40.5 + - - +
446B PHE 3.2 10.1 - - - +
447B VAL* 3.8 17.9 - - + +
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Residues in contact with PHE 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B GLU* 3.5 29.8 - - + +
228B GLU* 5.4 0.9 - - - -
230B GLN* 3.7 14.4 - - + -
231B TYR* 5.7 1.8 - - + -
261B MET* 3.8 35.0 - - + -
262B ARG* 1.3 78.4 - - - +
264B ASP* 1.3 59.6 + - - +
265B LEU* 3.4 18.9 + - + +
270B PRO* 3.6 26.9 - - + -
272B LEU* 5.9 2.0 - - + -
425B ILE* 3.9 36.6 - - + -
445B GLU* 3.2 9.1 - - - -
446B PHE* 2.9 55.1 + + + +
448B HIS* 4.6 2.0 - - + -
474B PHE* 4.6 4.5 - + - -
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Residues in contact with ASP 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B GLU* 2.8 21.5 + - - +
263B PHE* 1.3 69.0 - - - +
265B LEU* 1.3 60.6 + - - +
266B SER* 2.8 27.5 + - - -
267B ARG* 3.3 51.9 + - + +
268B SER* 3.5 13.2 + - - +
443B LEU 4.8 0.3 - - - +
444B GLY* 4.0 7.1 - - - +
445B GLU* 4.4 11.6 + - + +
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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