Contacts of the helix formed by residues 262 - 272 (chain A) in PDB entry 3TW4
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 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A LYS* 3.5 17.3 + - - -
224A ARG* 4.5 2.2 - - - +
226A PRO 3.8 0.2 - - - +
227A LEU* 3.3 16.1 - - + -
228A ALA* 2.4 55.8 + - - +
229A VAL* 5.8 0.4 - - + -
258A GLY* 4.8 0.4 - - - -
260A HIS 4.9 1.4 - - - +
261A CYS* 1.3 78.0 - - - +
263A PHE* 1.3 66.0 + - - +
264A THR 3.5 2.2 - - - -
265A ILE* 3.0 23.0 + - + +
266A LEU* 3.0 11.6 + - + +
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Residues in contact with PHE 263 (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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47A LEU* 4.8 12.6 - - + -
50A SER* 3.3 39.9 - - - -
51A LEU* 3.7 31.6 - - + -
228A ALA 4.1 1.4 + - - -
229A VAL* 5.6 4.7 - - + +
230A VAL 4.5 15.7 - - - +
232A SER* 3.8 23.1 - - - -
257A ASN* 3.4 30.0 + - - +
261A CYS* 3.2 11.3 - - + +
262A ASP* 1.3 76.5 - - - +
264A THR* 1.3 66.0 + - - +
266A LEU* 2.9 20.2 + - + +
267A ARG* 2.9 29.2 + - + -
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Residues in contact with THR 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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257A ASN 4.8 1.1 - - - -
258A GLY* 3.8 24.9 - - - -
262A ASP 3.5 0.4 - - - -
263A PHE* 1.3 80.6 - - - +
265A ILE* 1.3 55.3 + - - +
266A LEU 2.7 2.6 + - - -
267A ARG* 2.7 39.6 + - - +
268A ASN* 2.9 17.5 + - - +
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Residues in contact with ILE 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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221A ILE* 6.1 4.5 - - + -
258A GLY* 5.2 1.2 - - - +
262A ASP* 3.0 21.4 + - + +
264A THR* 1.3 76.4 - - - +
266A LEU* 1.3 59.1 + - - +
268A ASN* 4.6 6.3 - - - +
269A MET* 3.8 14.3 + - - +
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Residues in contact with LEU 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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47A LEU* 5.0 14.1 - - + -
51A LEU* 3.6 24.7 - - + -
229A VAL* 6.5 0.9 - - + -
262A ASP* 3.0 7.7 + - + +
263A PHE* 2.9 13.1 + - + +
264A THR 2.7 1.4 + - - -
265A ILE* 1.3 76.3 - - - +
267A ARG* 1.3 59.2 + - - +
268A ASN 3.0 1.8 - - - -
269A MET* 2.4 49.1 + - + -
270A LEU* 2.7 21.6 + - + -
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Residues in contact with ARG 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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51A LEU* 4.4 29.0 + - + +
257A ASN 5.7 4.6 - - - +
263A PHE* 2.9 28.3 + - + +
264A THR* 2.7 24.1 + - - +
266A LEU* 1.3 73.7 - - - +
268A ASN* 1.3 64.1 + - - +
270A LEU* 3.0 10.9 - - + +
271A ILE* 2.9 27.4 + - + +
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Residues in contact with ASN 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 THR 2.9 14.5 + - - +
265A ILE* 4.7 5.8 - - - +
266A LEU 2.7 3.0 + - - -
267A ARG* 1.3 80.1 - - - +
269A MET* 1.3 59.3 + - - +
270A LEU 2.9 5.5 + - - -
271A ILE* 3.3 9.2 + - - +
272A ARG 3.3 17.6 + - - +
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Residues in contact with MET 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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206A PHE* 4.7 20.2 - - + -
218A VAL* 5.9 6.5 - - + -
265A ILE 3.8 10.1 - - - +
266A LEU* 2.4 33.9 + - + +
268A ASN* 1.3 72.5 - - - +
270A LEU* 1.3 67.2 + - - +
272A ARG 4.6 2.7 - - - -
274A HIS* 3.2 36.3 - - + +
278A LEU* 6.4 1.8 - - - -
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Residues in contact with LEU 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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51A LEU* 4.9 7.6 - - + -
52A PHE* 5.5 10.3 - - + -
266A LEU* 2.7 19.4 + - + +
267A ARG* 3.0 21.8 - - + +
268A ASN 2.9 0.2 + - - -
269A MET* 1.3 84.9 - - - +
271A ILE* 1.3 74.7 + - - +
272A ARG* 2.8 4.7 + - - -
274A HIS 4.2 1.0 + - - -
275A MET* 3.9 19.8 - - + +
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Residues in contact with ILE 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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267A ARG* 2.9 13.5 + - + +
268A ASN* 3.3 2.7 + - - +
270A LEU* 1.3 81.1 - - - +
272A ARG* 1.3 82.8 + - + +
275A MET* 3.1 25.6 - - - +
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Residues in contact with ARG 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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30A PHE* 5.1 13.3 - - - +
268A ASN 3.3 15.3 + - - +
269A MET* 4.6 3.3 - - - -
270A LEU 2.8 4.2 + - - +
271A ILE* 1.3 97.6 + - + +
273A THR* 1.3 90.3 + - - +
274A HIS* 3.0 8.0 + - - +
275A MET* 3.8 14.0 - - - +
276A GLN* 3.4 24.4 - - - +
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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