Contacts of the strand formed by residues 260 - 265 (chain H) in PDB entry 1OAK
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 GLU 260 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251H VAL* 3.0 8.6 - - - +
252H ARG* 2.7 77.1 + - + +
254H PRO* 3.6 24.8 - - + +
257H LYS* 4.6 13.2 + - - +
258H GLY 5.1 0.8 - - - +
259H LEU* 1.3 80.4 - - - +
261H TRP* 1.3 63.4 + - - +
262H LEU* 3.6 5.3 + - + +
274H ASN* 6.1 0.9 - - - +
98L PHE* 4.2 1.3 - - - -
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Residues in contact with TRP 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249H ASP* 2.9 27.6 + - + +
250H TRP 3.9 2.7 - - - -
251H VAL* 4.0 20.0 - - + -
260H GLU* 1.3 71.7 - - - +
262H LEU* 1.3 67.4 + - - +
263H GLY* 3.5 32.6 + - - -
264H MET* 3.7 14.8 - - + -
272H ASP* 4.1 15.3 - - + -
273H TYR 4.4 2.0 - - - -
274H ASN* 2.8 36.1 + - - +
323H LEU* 4.6 6.5 - - + -
94L LEU* 3.5 23.3 - - + -
95L PRO* 3.4 33.7 - - + -
96L TRP* 3.4 51.5 + + + +
98L PHE* 3.9 11.1 - - + -
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Residues in contact with LEU 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250H TRP* 2.8 35.4 + - + +
252H ARG* 4.0 30.1 - - + +
260H GLU* 4.0 10.1 - - + +
261H TRP* 1.3 79.3 - - - +
263H GLY* 1.3 57.7 + - - +
273H TYR* 3.6 0.9 - - - -
274H ASN* 2.7 31.5 + - + +
277H LEU* 3.7 28.0 - - + +
281H LEU* 3.7 18.1 - - + +
294H LEU* 4.5 6.5 - - + -
296H MET* 5.4 3.1 - - - -
307H TYR* 3.6 35.4 - - + -
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Residues in contact with GLY 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249H ASP* 3.2 4.3 - - - +
250H TRP 2.9 24.4 + - - +
261H TRP* 3.5 15.8 + - - -
262H LEU* 1.3 83.2 - - - +
264H MET* 1.3 60.8 + - - -
272H ASP 3.1 14.1 - - - -
273H TYR* 4.1 2.5 - - - -
281H LEU* 4.4 0.6 - - - +
283H ILE* 3.5 12.3 - - - +
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Residues in contact with MET 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632A ARG* 4.1 11.4 - - - +
247H GLY* 4.3 1.1 - - - -
248H VAL 3.1 14.6 - - - +
249H ASP* 3.3 20.2 - - - +
261H TRP* 3.7 15.9 - - + -
263H GLY* 1.3 73.7 - - - +
265H ILE* 1.3 65.7 + - - +
266H TRP* 3.2 61.0 - - + +
271H THR* 3.3 6.4 - - - -
272H ASP* 2.9 41.6 + - + +
283H ILE* 3.5 8.6 - - - +
312H ASP* 3.5 16.4 - - - +
314H ALA* 4.0 12.3 - - + -
96L TRP* 5.8 0.2 - - - +
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Residues in contact with ILE 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243H LEU* 6.3 0.2 - - + -
246H TYR 4.6 0.2 - - - +
247H GLY* 3.3 18.4 - - - -
248H VAL* 3.0 16.7 + - + +
264H MET* 1.3 78.0 - - - +
266H TRP* 1.3 74.0 + - - +
269H GLY* 3.7 14.8 - - - +
270H SER 3.4 11.4 - - - +
271H THR* 3.9 3.1 - - + -
283H ILE* 3.6 38.8 - - + +
284H THR* 3.9 8.5 - - - -
285H LYS* 3.6 34.3 + - + -
292H VAL* 4.0 15.9 - - + -
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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