Contacts of the helix formed by residues 265 - 274 (chain D) in PDB entry 1C2O
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 ASN 265 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263D GLY* 3.1 8.4 - - - +
264D GLY* 1.3 80.0 + - - +
266D ASP* 1.4 70.6 + - - +
267D THR* 3.1 33.2 + - - -
268D GLU* 3.1 44.0 + - + +
269D LEU* 3.0 22.8 + - - +
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Residues in contact with ASP 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D LEU* 3.2 29.7 - - + +
162D PRO 5.5 2.4 - - - +
164D SER* 5.0 10.3 - - - -
166D GLU* 5.1 1.1 - - - +
245D ARG* 3.1 31.0 + - - -
264D GLY* 4.0 3.5 - - - -
265D ASN* 1.4 75.8 + - - +
267D THR* 1.3 52.9 + - - +
269D LEU* 2.9 13.0 + - - +
270D ILE* 2.7 41.5 + - + +
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Residues in contact with THR 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D ARG* 5.3 2.2 - - - +
166D GLU* 3.3 41.3 + - + +
265D ASN* 3.1 11.4 + - - -
266D ASP* 1.3 78.7 - - - +
268D GLU* 1.3 53.9 + - - +
270D ILE* 3.3 2.2 + - - +
271D ALA* 2.7 39.2 + - + +
274D ARG* 5.1 3.5 + - - +
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Residues in contact with GLU 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D PRO* 5.8 5.4 - - + -
263D GLY 6.0 0.2 - - - -
265D ASN* 3.1 39.6 + - + +
267D THR* 1.3 76.3 - - - +
269D LEU* 1.3 53.7 - - - +
271D ALA* 3.4 7.0 - - - +
272D CYS* 2.7 37.3 + - - +
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Residues in contact with LEU 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D LEU* 3.9 26.2 - - + -
245D ARG* 5.5 0.7 - - - +
249D THR* 4.3 22.9 - - + -
252D ALA* 3.2 33.7 - - + -
257D CYS* 4.3 2.0 - - + +
258D PRO* 4.5 22.4 - - + +
265D ASN 3.0 11.4 + - - +
266D ASP* 2.9 17.0 + - - +
268D GLU* 1.3 77.4 - - - +
270D ILE* 1.3 60.1 + - + +
272D CYS* 3.3 6.5 + - - +
273D LEU* 2.9 34.6 + - + +
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Residues in contact with ILE 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D PHE* 3.3 33.7 - - + -
159D LEU* 5.0 1.1 - - + -
161D LEU* 3.4 34.5 - - + -
164D SER* 4.6 2.5 - - - +
166D GLU* 3.7 33.4 - - + +
167D ALA* 3.3 25.1 - - + +
266D ASP* 2.7 26.2 + - + +
267D THR 4.0 1.8 - - - +
269D LEU* 1.3 70.1 - - - +
271D ALA* 1.3 57.0 + - - +
273D LEU* 2.9 8.4 + - + +
274D ARG* 2.7 47.7 + - - +
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Residues in contact with ALA 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D THR* 2.7 25.6 + - + +
268D GLU* 3.4 8.5 - - - +
270D ILE* 1.3 73.3 - - - +
272D CYS* 1.3 64.8 + - - +
274D ARG* 3.1 25.4 + - - +
275D THR* 3.3 13.9 - - - +
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Residues in contact with CYS 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D GLY 4.0 2.7 - - - -
257D CYS* 2.0 57.8 - - + -
258D PRO* 4.1 8.5 - - + -
259D PRO* 4.5 6.5 - - + -
268D GLU 2.7 20.7 + - - +
269D LEU* 3.4 5.8 - - - +
271D ALA* 1.3 75.3 - - - +
273D LEU* 1.4 61.5 + - - +
275D THR* 3.0 29.0 + - - -
276D ARG* 3.6 13.5 - - - +
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Residues in contact with LEU 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ARG* 2.8 19.9 + - - -
47D PHE* 3.8 13.5 - - + -
159D LEU* 4.1 28.5 - - + -
161D LEU* 5.3 1.1 - - + -
248D ALA 5.1 0.9 - - - +
251D LEU* 4.1 11.0 - - + -
252D ALA* 3.8 13.0 - - + -
255D VAL* 4.0 14.1 - - + -
257D CYS* 3.5 5.8 - - + -
269D LEU* 2.9 35.5 + - + +
270D ILE* 2.9 14.3 + - + +
272D CYS* 1.4 74.8 - - - +
274D ARG* 1.3 60.6 + - - +
275D THR 3.1 1.6 + - - -
276D ARG* 3.2 11.6 + - - +
281D LEU* 3.6 33.0 - - + +
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Residues in contact with ARG 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D GLY* 3.1 36.3 - - - +
44D SER* 3.3 30.1 + - - +
46D ARG* 2.8 57.6 + - + +
47D PHE* 4.6 2.0 - - + -
48D MET* 4.3 5.0 - - - +
165D ARG* 5.9 0.8 - - - +
166D GLU* 3.4 42.6 + - - +
267D THR* 5.1 3.4 + - - +
270D ILE* 2.7 30.3 + - - +
271D ALA* 3.1 20.0 + - - +
273D LEU* 1.3 74.1 - - - +
275D THR* 1.3 56.4 + - - +
276D ARG 3.5 0.2 - - - -
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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