Contacts of the strand formed by residues 260 - 269 (chain C) in PDB entry 2HJ9
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 VAL 260 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B ARG* 3.5 37.2 - - - +
256C VAL* 3.6 3.3 - - - +
257C VAL 2.9 31.6 + - - +
258C ASN* 3.6 9.6 - - + +
259C ALA* 1.3 82.3 - - - +
261C THR* 1.3 73.4 + - - +
262C THR* 3.5 4.3 + - - +
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Residues in contact with THR 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C PRO* 4.0 26.0 - - + -
255C ILE 3.8 6.7 - - - +
256C VAL* 3.8 15.3 - - + +
259C ALA 4.3 0.8 + - - -
260C VAL* 1.3 82.6 - - - +
262C THR* 1.3 72.2 + - - +
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Residues in contact with THR 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C TYR* 3.8 32.1 - - + -
255C ILE* 2.8 23.5 + - + +
257C VAL* 3.8 27.8 - - + +
260C VAL* 3.8 9.0 - - + +
261C THR* 1.3 85.1 - - - +
263C GLU* 1.3 58.5 + - - +
264C LEU* 3.1 31.9 + - - +
265C CYS* 5.9 0.2 - - - -
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Residues in contact with GLU 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C TYR* 2.5 40.4 + - + +
157C ASN* 2.7 25.6 + - - +
166C HIS* 4.1 0.5 + - - -
214C VAL 3.8 0.3 - - - +
215C ALA* 4.1 17.1 - - + +
216C ASN* 2.7 43.6 + - + +
262C THR* 1.3 73.3 - - - +
264C LEU* 1.3 59.7 + - - +
265C CYS* 3.9 3.8 + - - -
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Residues in contact with LEU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C PHE* 5.5 0.4 - - + -
155C TYR* 3.3 47.1 - - + +
166C HIS* 4.5 1.3 - - + +
168C LEU* 5.0 1.8 - - + -
192C LEU* 3.6 20.6 - - + -
213C LEU* 4.2 9.4 - - + -
214C VAL 3.2 9.9 - - - +
215C ALA* 4.0 6.1 - - + -
220C LEU* 3.8 28.5 - - + -
254C PRO* 3.7 0.9 - - - +
255C ILE* 2.8 50.9 + - + +
262C THR* 3.1 20.3 + - + +
263C GLU* 1.3 80.0 - - - +
265C CYS* 1.3 60.9 - - - +
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Residues in contact with CYS 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C VAL 3.7 0.3 - - - +
213C LEU* 3.5 8.3 - - - +
214C VAL* 2.9 45.2 + - + +
216C ASN 5.1 4.3 - - - +
252C GLU* 3.3 29.8 - - - +
253C THR 3.4 6.1 - - - +
254C PRO* 3.8 22.4 - - - -
255C ILE* 4.3 0.9 - - - +
262C THR 5.9 0.4 - - - -
263C GLU 3.9 3.3 + - - -
264C LEU* 1.3 79.2 - - - +
266C LEU* 1.3 62.2 + - - +
267C LEU* 5.1 0.2 - - + -
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Residues in contact with LEU 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ILE* 4.0 25.1 - - + -
64C PHE* 4.1 9.2 - - + -
199C MET* 4.1 7.6 - - + -
202C LEU* 3.9 33.0 - - + -
211C VAL* 4.6 9.4 - - + -
212C VAL 3.9 12.6 - - - +
213C LEU* 3.9 24.9 - - + +
251C ILE 3.3 3.1 - - - +
252C GLU* 3.6 0.7 - - - -
253C THR* 2.7 43.5 + - - +
255C ILE* 3.0 35.2 - - + +
265C CYS* 1.3 71.0 - - - +
267C LEU* 1.3 61.9 + - - +
268C THR* 3.9 2.9 + - + +
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Residues in contact with LEU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C ASN 3.8 0.3 - - - +
211C VAL* 3.2 6.9 - - - +
212C VAL* 2.7 45.0 + - + +
214C VAL* 4.4 25.8 - - + -
235C VAL* 4.1 35.0 - - + +
236C LEU* 4.4 15.3 - - + -
238C ARG* 5.9 2.9 - - + -
250C VAL* 4.4 9.6 - - + -
251C ILE 3.3 2.7 - - - +
252C GLU* 3.1 49.4 - - + +
266C LEU* 1.3 71.9 - - - +
268C THR* 1.3 62.6 + - - +
269C VAL* 4.2 1.8 + - - +
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Residues in contact with THR 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C THR* 3.8 9.9 - - - +
60C ILE* 3.6 40.1 - - + +
208C VAL* 4.0 20.2 - - + -
210C ASN 3.5 2.7 - - - -
211C VAL* 3.8 15.9 - - + -
249C LEU 3.4 1.5 - - - +
250C VAL* 3.2 7.8 - - - +
251C ILE* 2.9 51.3 + - - +
253C THR* 5.1 1.8 + - - +
266C LEU* 5.1 3.8 - - + +
267C LEU* 1.3 75.2 - - - +
269C VAL* 1.3 62.6 + - - +
270C GLN* 5.0 1.6 + - - -
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Residues in contact with VAL 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C VAL* 3.6 0.9 - - - +
209C ASP* 2.9 28.8 + - + +
210C ASN* 3.0 21.5 + - + +
212C VAL* 5.6 1.6 - - + -
230C TYR* 3.6 40.8 - - + +
235C VAL* 3.9 37.2 - - + -
248C LEU 4.3 16.4 - - - +
249C LEU 3.6 3.4 - - - +
250C VAL* 4.5 7.9 - - + -
267C LEU 4.7 1.6 - - - +
268C THR* 1.3 75.8 - - - +
270C GLN* 1.3 71.8 + - - +
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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