Contacts of the helix formed by residues 263 - 272 (chain C) in PDB entry 2ATW
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 ASP 263 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261C ASP* 2.9 15.9 + - - +
262C ASP* 1.3 76.2 - - - +
264C PRO* 1.3 73.1 - - - +
265C ALA* 3.4 14.8 + - - +
266C ARG* 3.0 62.9 + - + +
267C PHE* 3.0 11.4 + - - +
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Residues in contact with PRO 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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261C ASP 5.1 0.2 - - - +
262C ASP 3.0 11.6 - - - +
263C ASP* 1.3 89.3 - - - +
265C ALA* 1.3 57.9 + - - +
267C PHE* 3.2 10.5 + - + +
268C VAL* 2.9 34.5 + - - +
282C VAL* 5.5 2.0 - - + -
285C GLN* 6.0 2.7 - - + +
319C TRP* 3.4 45.0 - - + +
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Residues in contact with ALA 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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263C ASP* 3.2 13.5 + - - +
264C PRO* 1.3 79.6 - - - +
266C ARG* 1.3 61.9 + - + +
268C VAL* 3.6 1.7 + - - +
269C ALA* 3.3 16.5 + - - +
280C VAL* 3.7 44.5 - - + +
282C VAL* 4.5 16.9 - - + +
319C TRP* 6.3 0.7 - - - -
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Residues in contact with ARG 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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261C ASP* 3.3 33.5 + - + -
263C ASP* 3.0 38.3 + - - +
265C ALA* 1.3 74.8 - - + +
267C PHE* 1.3 61.1 - - - +
269C ALA* 3.2 6.6 + - - +
270C ASN* 2.8 39.8 + - - +
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Residues in contact with PHE 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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208C VAL* 5.6 0.9 - - + -
209C ALA* 5.3 2.7 - - + -
221C ALA* 3.8 27.4 - - + -
258C ILE* 4.3 2.7 - - + -
259C ASP 3.9 13.5 - - - -
260C TYR* 3.8 35.9 - + - -
261C ASP* 3.5 26.4 - - - +
263C ASP 3.0 5.8 + - - +
264C PRO* 3.2 12.8 + - + +
266C ARG* 1.3 78.1 - - - +
268C VAL* 1.3 55.9 + - - +
270C ASN* 3.2 2.7 + - - +
271C ALA* 2.9 27.0 + - - +
316C LEU* 4.1 20.2 - - + -
317C THR* 3.7 39.9 - - + -
319C TRP* 5.9 2.0 - + - -
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Residues in contact with VAL 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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264C PRO 2.9 20.0 + - - +
265C ALA* 4.0 5.2 - - - +
266C ARG 3.3 0.4 - - - -
267C PHE* 1.3 74.3 - - - +
269C ALA* 1.3 64.4 + - - +
271C ALA* 3.2 11.1 + - - +
272C LEU* 3.2 17.0 + - + +
280C VAL* 4.5 5.6 - - + -
290C ALA* 4.8 5.2 - - + -
292C VAL* 3.6 31.0 - - + -
317C THR* 4.1 15.9 - - + +
319C TRP* 3.7 38.6 - - + -
321C ILE* 4.1 19.7 - - + -
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Residues in contact with ALA 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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265C ALA 3.3 11.7 + - - +
266C ARG* 3.2 11.5 + - - +
268C VAL* 1.3 79.9 - - - +
270C ASN* 1.3 67.6 + - - +
272C LEU* 3.4 9.1 + - - +
273C SER* 3.8 3.1 + - - -
275C ALA 4.9 0.2 - - - +
277C VAL* 3.5 37.7 - - + +
280C VAL* 3.8 16.4 - - + +
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Residues in contact with ASN 270 (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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258C ILE* 3.5 9.8 - - + +
259C ASP* 3.3 42.4 + - - +
260C TYR 4.6 0.2 + - - -
261C ASP* 4.1 16.8 + - - +
266C ARG* 2.8 22.5 + - - +
267C PHE 3.5 4.5 - - - +
269C ALA* 1.3 81.7 - - - +
271C ALA* 1.3 57.3 + - - +
273C SER* 3.0 31.4 - - - -
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Residues in contact with ALA 271 (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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219C LYS* 2.9 32.7 + - - +
258C ILE* 3.7 13.0 - - + +
267C PHE 2.9 16.9 + - - +
268C VAL 3.2 5.6 + - - +
270C ASN* 1.3 77.1 - - - +
272C LEU* 1.3 57.4 + - - +
273C SER 3.2 0.6 - - - +
313C ALA* 3.6 17.3 - - + +
316C LEU* 4.1 13.5 - - + -
317C THR* 3.7 21.5 - - + -
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Residues in contact with LEU 272 (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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268C VAL* 3.2 14.2 + - + +
269C ALA 3.8 8.3 - - - +
270C ASN 3.2 0.8 - - - -
271C ALA* 1.3 72.8 - - - +
273C SER* 1.3 68.6 + - - +
275C ALA* 3.0 19.6 + - + +
277C VAL* 4.5 10.1 - - + -
292C VAL* 3.5 34.1 - - + -
294C VAL* 5.1 3.8 - - + -
302C ALA* 3.8 10.8 - - - +
309C ASN* 2.9 35.8 + - - +
310C ALA* 4.2 6.7 - - - -
313C ALA* 3.9 17.0 - - + -
321C ILE* 4.0 19.1 - - + -
323C ILE* 3.8 17.3 - - + -
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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