Contacts of the helix formed by residues 260 - 271 (chain T) in PDB entry 3P71
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 SER 260 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231T VAL* 3.5 8.5 - - - +
232T ASN* 3.7 13.5 - - - -
258T CYS 3.6 1.4 - - - -
259T LYS* 1.3 90.4 + - - +
261T LEU* 1.3 64.2 + - - +
262T GLU* 3.6 10.5 + - - +
263T SER* 3.0 32.0 + - - -
264T GLN* 3.1 13.9 + - - +
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Residues in contact with LEU 261 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231T VAL* 3.6 8.5 - - + +
232T ASN* 4.4 6.0 + - - +
260T SER* 1.3 74.2 - - - +
262T GLU* 1.3 65.3 + - + +
264T GLN* 3.4 5.3 + - - +
265T LYS* 3.1 36.0 + - - +
278T ALA* 3.8 25.6 - - + +
279T VAL* 3.6 8.5 - - - -
280T ASP* 3.6 39.9 - - + +
283T GLU* 4.4 9.9 - - - +
316T CYS* 3.7 20.9 - - + -
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Residues in contact with GLU 262 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260T SER* 3.2 9.7 + - - +
261T LEU* 1.3 80.3 - - + +
263T SER* 1.3 59.3 + - - +
265T LYS* 3.2 34.4 + - - +
266T GLU* 3.0 28.6 + - - +
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Residues in contact with SER 263 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256T GLU 5.9 0.2 - - - -
257T THR* 3.6 9.3 + - - +
259T LYS* 3.6 21.3 + - - +
260T SER* 3.0 34.7 + - - -
262T GLU* 1.3 79.6 - - - +
264T GLN* 1.3 52.8 + - - +
266T GLU* 3.8 6.8 - - - +
267T ARG* 2.8 35.0 + - - +
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Residues in contact with GLN 264 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227T ASN* 3.9 7.2 + - - -
229T GLU* 3.0 26.3 + - - +
230T GLN 3.2 21.8 + - - -
231T VAL* 4.3 3.8 - - + -
257T THR 3.6 17.8 + - - +
258T CYS* 4.2 1.6 - - - +
260T SER 3.1 22.4 + - - +
261T LEU* 3.6 7.6 - - - +
262T GLU 3.2 0.2 - - - -
263T SER* 1.3 75.7 + - - +
265T LYS* 1.3 62.6 + - - +
267T ARG* 3.5 30.2 + - - +
268T LEU* 3.5 28.2 + - - +
278T ALA* 4.8 1.1 - - + -
316T CYS* 3.7 15.9 - - - -
318T CYS* 3.9 15.6 - - - -
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Residues in contact with LYS 265 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261T LEU* 3.1 19.6 + - - +
262T GLU* 3.2 37.5 + - - +
264T GLN* 1.3 74.0 - - - +
266T GLU* 1.3 57.6 + - - +
268T LEU* 3.3 6.3 + - + +
269T LEU* 3.1 37.3 + - + +
276T ALA* 3.7 24.7 - - + +
277T SER* 3.9 8.3 - - - +
278T ALA* 3.7 38.0 + - + +
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Residues in contact with GLU 266 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262T GLU 3.0 18.8 + - - +
263T SER* 3.8 8.3 - - - +
265T LYS* 1.3 74.6 - - - +
267T ARG* 1.3 63.9 + - - +
269T LEU* 4.2 17.0 - - - +
270T SER* 2.8 51.7 + - - +
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Residues in contact with ARG 267 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201T LEU* 3.5 20.1 + - - +
206T PRO 5.7 1.3 - - - -
209T SER* 2.9 33.8 + - - -
210T ALA* 5.9 2.2 - - - +
213T LEU* 4.0 13.1 - - + +
227T ASN* 3.4 16.0 - - - +
229T GLU* 2.7 37.2 + - - -
254T GLY* 6.2 0.2 - - - -
257T THR* 3.5 36.3 + - - +
263T SER 2.8 21.2 + - - +
264T GLN* 3.5 17.1 + - - +
265T LYS 3.3 0.2 - - - -
266T GLU* 1.3 74.6 - - - +
268T LEU* 1.3 62.4 + - + +
270T SER* 4.9 1.3 - - - -
271T ASN* 2.8 43.1 + - - +
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Residues in contact with LEU 268 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201T LEU* 5.9 0.2 - - + -
213T LEU* 3.6 35.4 - - + -
225T PHE* 4.7 10.8 - - + +
227T ASN* 5.0 9.9 - - + +
264T GLN 3.5 15.9 + - - +
265T LYS* 3.3 8.3 + - - +
266T GLU 3.2 0.4 - - - -
267T ARG* 1.3 78.8 - - + +
269T LEU* 1.3 63.0 - - - +
271T ASN* 3.4 4.7 + - - -
273T TRP* 3.1 31.2 + - + +
276T ALA* 4.1 12.8 - - + -
277T SER 5.1 0.4 - - - +
318T CYS* 4.0 26.0 - - + -
319T TRP* 4.3 1.3 - - - +
320T ALA* 3.8 36.1 - - + +
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Residues in contact with LEU 269 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265T LYS* 3.1 26.0 + - + +
266T GLU* 3.5 20.2 + - - +
268T LEU* 1.3 71.9 - - - +
270T SER* 1.3 64.4 + - - +
271T ASN 3.1 2.7 + - - -
272T GLY* 3.4 9.5 + - - -
273T TRP 3.5 20.6 + - - +
274T GLU 3.5 29.2 - - - +
275T THR* 3.9 14.1 - - - -
276T ALA* 4.0 9.0 - - + +
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Residues in contact with SER 270 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214T LYS* 5.4 2.9 + - - -
266T GLU* 2.8 43.3 + - - +
267T ARG* 4.3 4.5 - - - -
269T LEU* 1.3 76.2 - - - +
271T ASN* 1.3 66.0 + - - +
272T GLY 3.4 2.8 + - - -
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Residues in contact with ASN 271 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210T ALA* 3.9 34.9 - - - +
213T LEU* 3.5 21.7 - - + +
214T LYS* 3.7 28.5 + - - +
217T ALA* 3.5 9.2 - - - +
267T ARG* 2.8 36.1 + - - +
268T LEU 3.4 5.8 + - - +
269T LEU 3.1 1.4 - - - -
270T SER* 1.3 84.7 - - - +
272T GLY* 1.3 54.2 + - - -
273T TRP* 3.3 15.5 + - - -
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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