Contacts of the helix formed by residues 263 - 272 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A ASP* 3.0 7.8 + - - +
262A ASP* 1.3 79.4 - - - +
264A PRO* 1.3 67.5 - - - +
265A ALA* 3.3 13.4 + - - +
266A ARG* 3.0 65.1 + - - +
267A PHE* 2.8 28.2 + - - +
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Residues in contact with PRO 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ASP 3.3 10.3 - - - +
263A ASP* 1.3 88.9 - - - +
265A ALA* 1.3 66.4 + - - +
267A PHE* 3.1 7.4 + - + -
268A VAL* 2.8 32.0 + - + +
282A VAL* 5.0 7.0 - - + -
288A ARG* 5.6 1.8 - - - +
319A TRP* 3.6 47.6 - - + +
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Residues in contact with ALA 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ASP* 3.3 11.8 + - - +
264A PRO* 1.3 78.5 - - - +
266A ARG* 1.3 59.6 + - + +
269A ALA* 3.0 29.6 + - - +
280A VAL* 3.6 42.2 - - + +
281A SER* 5.8 0.2 - - - -
282A VAL* 5.1 12.2 - - + +
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Residues in contact with ARG 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A ASP* 3.1 37.7 + - + +
263A ASP* 3.0 38.9 + - - +
265A ALA* 1.3 75.6 - - + +
267A PHE* 1.3 61.0 + - - +
269A ALA* 3.3 4.7 + - - +
270A ASN* 2.8 40.6 + - - +
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Residues in contact with PHE 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A VAL* 5.8 0.4 - - + -
209A ALA* 5.1 3.1 - - + -
221A ALA* 3.7 28.0 - - + -
258A ILE* 4.3 3.4 - - + -
259A ASP 4.0 13.7 - - - -
260A TYR* 3.7 30.1 - + - -
261A ASP* 3.4 30.9 - - - +
263A ASP 2.8 13.9 + - - +
264A PRO* 3.8 6.5 - - + +
266A ARG* 1.3 73.1 - - - +
268A VAL* 1.3 52.3 + - + +
270A ASN* 2.9 5.7 + - - +
271A ALA* 2.7 33.1 + - - +
316A LEU* 3.9 23.1 - - + -
317A THR* 3.7 37.2 - - + -
319A TRP* 6.0 1.6 - + - -
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Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A PRO* 2.8 25.4 + - + +
265A ALA* 4.0 2.9 - - - +
267A PHE* 1.3 71.3 - - - +
269A ALA* 1.3 65.2 + - - +
271A ALA* 3.2 9.6 + - - +
272A LEU* 3.3 15.6 + - + +
280A VAL* 4.3 9.0 - - + -
290A ALA* 4.7 9.4 - - + -
292A VAL* 3.9 25.1 - - + -
317A THR* 4.1 15.7 - - - +
319A TRP* 3.7 37.2 - - + -
321A ILE* 3.8 21.8 - - + -
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Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ALA 3.0 20.2 + - - +
266A ARG* 3.7 6.1 - - - +
268A VAL* 1.3 78.0 - - - +
270A ASN* 1.3 66.5 + - - +
272A LEU* 3.4 7.8 + - - +
273A SER* 3.9 3.8 + - - -
275A ALA 5.0 0.7 - - - +
277A VAL* 3.6 43.8 - - + +
280A VAL* 3.8 9.8 - - + +
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Residues in contact with ASN 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ILE* 3.4 12.1 - - + +
259A ASP* 3.2 43.3 + - - +
261A ASP* 4.1 17.4 + - - +
266A ARG* 2.8 26.8 + - - +
267A PHE 3.3 3.8 - - - +
269A ALA* 1.3 80.1 - - - +
271A ALA* 1.3 62.6 + - - +
273A SER* 3.0 24.8 + - - -
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Residues in contact with ALA 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A LYS* 3.0 31.2 + - - +
258A ILE* 3.6 14.7 - - + +
267A PHE* 2.7 18.6 + - + +
268A VAL 3.2 3.8 + - - +
270A ASN* 1.3 75.7 - - - +
272A LEU* 1.3 56.1 + - - +
273A SER 3.1 1.2 + - - +
313A ALA* 3.7 19.7 - - + -
316A LEU* 4.0 11.7 - - + -
317A THR* 3.6 24.5 - - + -
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A VAL* 3.3 15.4 + - + +
269A ALA 3.8 6.7 - - - +
270A ASN 3.2 0.8 - - - -
271A ALA* 1.3 72.6 - - - +
273A SER* 1.3 66.0 + - - +
275A ALA* 3.0 16.8 + - + +
277A VAL* 4.2 12.8 - - + -
292A VAL* 3.7 33.2 - - + -
294A VAL* 5.2 2.2 - - + -
302A ALA* 3.8 22.4 - - + +
309A ASN* 2.7 27.1 + - - +
310A ALA* 4.0 7.4 - - - -
313A ALA* 3.7 20.4 - - + -
321A ILE* 4.0 17.7 - - + -
323A ILE* 3.9 15.0 - - + -
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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