Contacts of the helix formed by residues 258 - 270 (chain C) in PDB entry 2IGT
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 258 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257C ALA* 1.3 77.1 - - - +
259C PHE* 1.3 70.8 + - - +
260C TYR* 2.9 35.7 + - - +
261C SER* 3.0 24.2 + - - -
262C MSE 3.7 3.1 + - - -
281C GLU* 6.0 0.7 - - - -
302C LEU* 3.9 5.4 - - - +
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Residues in contact with PHE 259 (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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12C VAL* 3.5 27.6 - - + -
13C PRO* 3.4 26.5 - - + -
15C ILE* 5.4 3.6 - - + -
258C SER* 1.3 79.9 + - - +
260C TYR* 1.3 91.1 + + - +
261C SER 3.2 0.2 + - - -
262C MSE 3.3 4.7 + - - +
263C HIS* 2.8 29.3 + - - +
279C SER* 4.3 1.6 - - - -
280C GLY* 3.3 37.7 - - - +
281C GLU* 3.9 29.1 + - + -
302C LEU* 3.9 20.5 - - + +
303C PHE 4.8 1.3 - - - +
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Residues in contact with TYR 260 (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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12C VAL* 3.7 31.7 + - + -
13C PRO* 3.8 20.1 - - + +
258C SER* 2.9 20.8 + - - +
259C PHE* 1.3 108.5 - + - +
261C SER* 1.3 57.3 + - - +
263C HIS* 3.4 8.8 - + - +
264C GLU* 2.8 44.3 + - + +
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Residues in contact with SER 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C PHE* 6.1 0.4 - - - -
257C ALA* 4.4 8.8 - - - +
258C SER* 3.0 21.1 + - - -
260C TYR* 1.3 76.9 - - - +
262C MSE 1.3 78.2 + - - +
264C GLU* 4.6 2.9 - - - +
265C LEU* 3.2 24.6 + - - +
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Residues in contact with MSE 262 (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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226C LEU* 4.4 16.8 - - + -
227C PHE* 4.7 6.1 - - + -
230C LEU* 3.9 25.6 - - + -
250C LEU* 3.9 21.4 - - + +
252C ALA* 4.3 16.4 - - + -
255C ILE* 5.7 1.6 - - + -
257C ALA* 4.3 15.7 - - + -
258C SER 4.2 1.3 - - - +
259C PHE* 3.3 6.9 + - - +
261C SER* 1.3 89.3 - - - +
263C HIS* 1.3 60.1 + - - +
265C LEU* 3.5 8.1 + - + +
266C MSE 2.9 31.4 + - - +
302C LEU* 3.8 31.6 - - + -
303C PHE* 4.8 4.9 - - - +
304C SER* 3.9 11.7 + - - -
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Residues in contact with HIS 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLU* 2.7 38.3 + - + +
11C HIS 4.4 0.4 - - - -
12C VAL* 3.7 25.0 - - + +
259C PHE 2.8 18.2 + - - +
260C TYR* 3.4 12.3 - + - +
261C SER 3.3 0.2 - - - -
262C MSE 1.3 77.1 - - - +
264C GLU* 1.3 72.9 + - + +
266C MSE 3.2 2.8 + - - +
267C ARG* 2.8 32.9 + - - +
277C VAL* 3.4 35.0 - - + +
279C SER* 2.7 36.0 + - - +
304C SER* 4.0 1.1 - - - -
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Residues in contact with GLU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 5.5 2.9 - - - +
10C GLU* 4.8 4.2 - - - +
260C TYR* 2.8 32.6 + - + +
261C SER* 4.6 3.4 - - - +
263C HIS* 1.3 81.5 - - + +
265C LEU* 1.3 65.9 + - - +
267C ARG* 3.5 25.3 + - - +
268C GLU* 3.0 25.1 + - - +
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Residues in contact with LEU 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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230C LEU* 3.8 26.0 - - + -
231C PRO* 4.1 34.1 - - + -
234C LEU* 3.6 25.6 - - + -
250C LEU* 5.5 0.2 - - + -
261C SER 3.2 21.0 + - - +
262C MSE 3.7 8.5 - - + +
264C GLU* 1.3 77.6 - - - +
266C MSE 1.3 58.0 + - - +
268C GLU* 3.3 5.3 + - + +
269C THR* 2.8 38.1 + - - +
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Residues in contact with MSE 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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234C LEU* 4.4 16.1 - - + +
248C LEU* 3.8 42.0 - - + +
250C LEU* 3.7 23.6 - - + +
262C MSE 2.9 12.0 + - - +
263C HIS 3.7 1.8 - - - +
265C LEU* 1.3 76.6 - - - +
267C ARG* 1.3 64.3 + - - +
269C THR* 3.2 6.9 + - - -
270C MSE 3.0 33.9 + - + +
277C VAL* 3.7 18.2 - - + -
304C SER* 3.1 47.8 - - - +
306C TRP* 4.3 7.9 - - + +
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Residues in contact with ARG 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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7C LEU* 3.6 37.9 + - + +
8C PRO* 2.8 51.5 + - + +
9C ALA* 4.5 2.8 - - - +
10C GLU* 3.6 46.0 + - - +
263C HIS* 2.8 21.5 + - - +
264C GLU* 3.7 20.9 + - - +
265C LEU 3.3 0.2 - - - -
266C MSE 1.3 76.4 - - - +
268C GLU* 1.3 61.6 + - - +
270C MSE 3.3 1.9 + - - -
271C ARG 3.2 16.8 + - - -
277C VAL* 4.1 19.2 - - + +
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Residues in contact with GLU 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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1C MSE 5.8 0.6 - - - +
2C GLN* 6.0 0.3 - - - -
3C ARG* 4.6 9.7 + - - +
7C LEU* 3.8 10.0 - - + +
264C GLU 3.0 17.2 + - - +
265C LEU* 3.8 7.4 - - + +
267C ARG* 1.3 73.4 - - - +
269C THR* 1.3 67.2 + - - +
271C ARG* 2.8 64.8 + - - +
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Residues in contact with THR 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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3C ARG* 4.1 7.6 + - - +
231C PRO 5.0 2.1 + - - -
234C LEU* 3.4 51.1 - - + +
235C ASP* 3.9 9.8 + - + +
238C ARG* 2.8 31.5 + - + -
248C LEU* 5.1 2.5 - - + -
265C LEU* 2.8 33.1 + - - +
266C MSE 3.2 9.2 + - - -
268C GLU* 1.3 75.5 - - - +
270C MSE 1.3 65.5 + - - +
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Residues in contact with MSE 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C PRO* 3.7 15.3 - - + +
238C ARG* 3.3 32.3 - - + +
241C LEU* 4.0 13.5 - - + -
248C LEU* 4.1 19.7 - - - -
266C MSE 3.0 22.6 + - + +
267C ARG 3.5 3.4 - - - -
268C GLU 3.1 0.4 - - - -
269C THR* 1.3 77.6 - - - +
271C ARG* 1.3 66.3 + - - +
272C GLY 3.2 0.5 + - - -
273C ALA* 3.0 32.7 + - + +
306C TRP* 3.6 64.8 - - + +
1006C ACY 4.3 2.7 - - - +
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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