Contacts of the strand formed by residues 260 - 265 (chain B) in PDB entry 2R8K
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 THR 260 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ILE* 3.8 13.5 - - + -
30B ASP 3.3 10.5 - - - -
31B MET* 3.4 31.6 - - + -
32B ASN* 3.2 7.3 - - - +
142B PHE* 5.8 1.3 - - + -
249B ARG* 3.1 53.8 + - - +
252B ILE* 4.7 9.9 - - + -
258B TYR 4.0 8.6 + - - +
259B THR* 1.3 81.9 - - - +
261B SER* 1.3 59.9 + - - +
281B ASP* 3.5 4.6 + - - +
282B ALA 3.4 5.0 + - - +
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Residues in contact with SER 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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28B HIS 4.1 0.2 - - - +
29B ILE* 3.7 2.8 - - - +
30B ASP* 3.0 35.0 + - - +
32B ASN* 2.8 23.4 + - - -
260B THR* 1.3 74.3 - - - +
262B CYS* 1.3 59.9 + - - +
275B SER* 3.1 27.8 - - - -
278B LYS 3.2 17.9 + - - -
279B LYS* 3.3 12.8 - - - +
280B PRO* 4.0 2.1 - - - +
281B ASP 4.0 0.3 + - - -
282B ALA 3.2 7.4 - - - +
4001B DTP 6.0 0.2 - - - -
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Residues in contact with CYS 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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27B ALA* 4.7 0.7 - - - -
28B HIS 3.4 12.6 - - - +
29B ILE* 4.0 4.5 - - + -
245B CYS* 3.4 25.6 - - - -
249B ARG* 3.3 25.4 - - - +
261B SER* 1.3 75.8 - - - +
263B GLY* 1.3 56.5 + - - +
264B LEU* 3.3 26.0 - - - -
275B SER* 3.8 7.8 - - - +
282B ALA 2.8 8.9 + - - -
283B GLN* 3.0 15.5 - - + +
284B THR 2.7 32.9 + - - +
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Residues in contact with GLY 263 (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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27B ALA* 3.3 3.6 - - - -
28B HIS 2.9 34.1 + - - -
262B CYS* 1.3 73.0 - - - +
264B LEU* 1.3 63.7 + - - +
271B CYS* 3.5 10.0 - - - +
274B ALA* 3.7 7.9 - - - -
275B SER* 3.6 22.4 - - - -
284B THR 3.4 5.4 - - - -
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Residues in contact with LEU 264 (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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25B CYS* 5.2 1.8 - - - -
26B ILE 3.5 4.5 - - - +
27B ALA* 4.1 12.6 - - + -
161B LEU* 5.0 2.0 - - + -
238B LEU* 3.8 21.3 - - + +
241B GLY* 3.8 6.3 - - - +
242B SER* 3.3 44.2 - - - +
245B CYS* 4.2 4.0 - - + -
262B CYS* 3.3 31.6 - - - -
263B GLY* 1.3 75.1 - - - +
265B SER* 1.3 63.6 + - - +
271B CYS* 5.2 0.2 - - - -
274B ALA* 4.4 1.1 - - - +
283B GLN* 3.6 17.0 - - + +
284B THR 3.1 10.1 + - - +
285B ILE* 3.8 7.0 - - + +
286B VAL* 3.0 29.3 + - - +
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Residues in contact with SER 265 (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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24B ALA 5.0 0.4 - - - -
25B CYS* 3.7 5.3 - - - -
26B ILE* 3.0 29.0 + - - +
238B LEU* 4.2 9.5 - - - +
264B LEU* 1.3 76.5 - - - +
266B SER* 1.3 61.0 + - - +
267B THR 3.0 13.9 + - - -
270B VAL* 3.4 21.2 - - - +
271B CYS* 2.9 27.8 + - - -
274B ALA* 5.9 0.2 - - - -
286B VAL* 3.9 18.4 - - - -
288B ASN* 5.0 0.9 - - - +
291B LEU* 4.8 2.5 - - - -
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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