Contacts of the helix formed by residues 269 - 286 (chain A) in PDB entry 2IAG
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 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A GLY 3.5 5.4 + - - -
268A VAL* 1.3 77.2 - - - +
270A GLU* 1.3 59.2 + - - +
271A GLU* 3.6 12.1 + - - +
272A MET* 3.2 19.1 + - - +
273A GLN* 2.8 25.3 + - - +
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Residues in contact with GLU 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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242A SER* 5.5 0.4 - - - -
243A PRO* 3.1 33.0 - - + +
244A ALA* 4.4 18.5 + - - +
269A SER* 1.3 74.9 - - - +
271A GLU* 1.3 71.6 + - - +
273A GLN* 3.8 16.2 - - - +
274A ALA* 3.0 23.4 + - - +
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Residues in contact with GLU 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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238A TRP* 5.4 1.4 - - - +
269A SER* 3.2 10.1 + - - +
270A GLU* 1.3 92.3 + - - +
272A MET* 1.3 60.8 + - - +
274A ALA* 3.9 7.9 - - - +
275A ARG* 3.3 28.0 + - - +
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Residues in contact with MET 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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109A ASP 3.7 24.7 - - - +
110A VAL* 3.8 14.6 - - + -
111A GLN* 3.9 35.4 - - + +
112A LEU* 4.3 4.5 - - + -
268A VAL* 3.6 23.3 - - + +
269A SER* 3.2 14.2 + - - +
271A GLU* 1.3 76.5 - - - +
273A GLN* 1.3 65.7 + - - +
274A ALA 3.2 0.2 - - - -
275A ARG* 3.3 24.5 + - - +
276A ALA* 3.0 22.0 + - - +
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Residues in contact with GLN 273 (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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243A PRO* 3.5 21.5 - - + +
260A LEU* 4.1 18.7 - - - +
263A LEU* 3.8 37.1 - - + +
264A GLU* 4.6 11.1 - - - +
268A VAL* 2.8 26.0 + - + +
269A SER 2.8 17.4 + - - +
270A GLU* 3.3 21.4 + - - +
272A MET* 1.3 76.8 - - - +
274A ALA* 1.3 55.7 + - - +
276A ALA* 3.2 4.3 + - - +
277A LEU* 2.9 36.8 + - + +
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Residues in contact with ALA 274 (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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238A TRP* 3.3 32.1 - - + +
241A LEU 3.6 18.8 - - - +
242A SER* 3.8 7.0 - - - -
243A PRO* 3.9 1.5 - - + +
270A GLU 3.0 15.9 + - - +
271A GLU* 3.9 9.4 - - - +
273A GLN* 1.3 72.3 - - - +
275A ARG* 1.3 65.4 + - - +
277A LEU* 3.3 2.5 + - - +
278A VAL* 3.1 28.8 + - - +
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Residues in contact with ARG 275 (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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108A PHE* 4.3 3.1 - - - +
109A ASP* 3.0 37.5 + - - +
110A VAL* 3.6 16.5 - - + +
238A TRP* 3.5 61.1 + - + +
271A GLU 3.3 16.0 + - - +
272A MET* 3.3 34.1 + - - +
274A ALA* 1.3 76.7 - - - +
276A ALA* 1.3 55.7 - - - +
278A VAL* 3.5 3.6 + - - +
279A LEU* 3.2 21.0 + - - +
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Residues in contact with ALA 276 (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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110A VAL* 4.2 16.3 - - + +
112A LEU* 4.8 6.1 - - + -
259A TYR* 3.6 19.3 - - - +
263A LEU* 4.2 15.9 - - + -
272A MET 3.0 13.1 + - - +
273A GLN* 3.5 8.5 - - - +
275A ARG* 1.3 74.4 - - - +
277A LEU* 1.3 59.0 + - - +
279A LEU* 3.4 11.7 - - + +
280A GLN* 2.9 32.2 + - - +
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Residues in contact with LEU 277 (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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181A TYR* 2.7 38.3 + - + +
241A LEU* 3.5 27.2 - - + +
243A PRO* 4.4 7.2 - - + -
246A LEU* 3.7 15.5 - - + -
255A TRP* 5.3 0.9 - - + -
256A LEU* 3.5 28.5 - - + -
259A TYR* 3.9 23.8 - - + -
260A LEU* 3.7 20.2 - - + -
263A LEU* 4.9 0.7 - - + -
273A GLN 2.9 24.8 + - - +
274A ALA* 3.3 4.5 + - - +
276A ALA* 1.3 75.7 - - - +
278A VAL* 1.3 59.5 + - - +
280A GLN* 3.5 4.2 + - + -
281A LEU* 2.9 11.4 + - - +
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Residues in contact with VAL 278 (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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108A PHE* 3.9 11.1 - - + -
207A PHE* 5.3 2.3 - - + -
210A LEU* 4.2 14.1 - - + -
234A LYS* 6.0 1.3 - - + -
237A LEU* 3.5 53.4 - - + +
238A TRP* 3.7 19.7 - - + +
241A LEU* 4.0 13.9 - - + -
274A ALA 3.1 17.5 + - - +
275A ARG 3.8 4.5 - - - +
276A ALA 3.3 0.2 - - - -
277A LEU* 1.3 74.9 - - - +
279A LEU* 1.3 64.9 + - - +
281A LEU* 3.2 11.0 + - + +
282A TRP* 3.1 17.0 + - - +
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Residues in contact with LEU 279 (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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104A MET* 3.7 35.7 - - + -
108A PHE* 3.7 42.5 - - + -
110A VAL* 4.1 17.7 - - + -
112A LEU* 5.8 0.9 - - + -
259A TYR* 5.0 2.2 - - - +
275A ARG 3.2 13.5 + - - +
276A ALA* 3.4 12.3 - - + +
278A VAL* 1.3 77.0 - - - +
280A GLN* 1.3 74.0 + - - +
282A TRP* 3.1 16.4 + - + +
283A ALA* 2.9 28.0 + - + +
600A HEM 6.1 0.9 - - - +
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Residues in contact with GLN 280 (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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124A MET* 4.0 9.0 - - - +
181A TYR* 3.6 4.9 - - - +
255A TRP* 3.7 23.8 - - + -
259A TYR* 3.6 36.6 + - + -
276A ALA 2.9 18.1 + - - +
277A LEU* 3.6 8.3 - - - +
278A VAL 3.4 0.2 - - - -
279A LEU* 1.3 89.3 - - - +
281A LEU* 1.3 60.1 + - - +
283A ALA* 4.1 6.7 - - - +
284A THR* 2.9 34.8 + - - +
600A HEM 3.3 44.3 + - - +
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Residues in contact with LEU 281 (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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173A LEU* 4.9 3.6 - - + -
177A TYR* 4.0 19.7 - - + -
181A TYR* 3.2 24.0 + - + +
203A VAL* 3.9 23.3 - - + -
207A PHE* 4.0 27.9 - - + -
237A LEU* 4.8 7.0 - - + -
241A LEU* 4.1 13.9 - - + -
277A LEU 2.9 16.0 + - - +
278A VAL* 3.4 14.6 - - + +
279A LEU 3.2 0.4 - - - -
280A GLN* 1.3 74.3 - - - +
282A TRP* 1.3 58.8 + - - +
284A THR* 4.0 1.3 - - - -
285A GLN* 3.0 58.4 + - + +
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Residues in contact with TRP 282 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A LEU* 6.5 0.9 - - + -
107A ILE* 6.2 2.2 - - + -
108A PHE* 3.4 42.8 - + + -
207A PHE* 3.8 23.5 - + + -
211A ASP* 4.0 18.7 + - - -
214A LEU* 3.5 33.6 - - + +
278A VAL 3.1 4.6 + - - +
279A LEU* 3.1 15.2 + - + +
281A LEU* 1.3 77.2 - - - +
283A ALA* 1.3 80.0 + - + +
286A GLY* 2.8 36.9 + - - -
287A ASN* 4.8 2.0 + - - -
480A ARG* 5.5 0.8 - - - +
483A PHE* 4.0 28.9 - + + -
600A HEM 6.5 1.3 - - - -
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Residues in contact with ALA 283 (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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279A LEU* 2.9 17.7 + - + +
280A GLN* 3.2 20.8 + - - +
282A TRP* 1.3 95.0 - - + +
284A THR* 1.3 61.2 + - - +
286A GLY 4.7 0.7 + - - -
287A ASN* 5.2 5.0 + - - -
600A HEM 3.5 47.7 + - + +
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Residues in contact with THR 284 (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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180A LEU* 3.7 7.1 - - + +
181A TYR* 4.8 3.1 - - - -
255A TRP* 3.8 25.1 - - + +
280A GLN* 2.9 25.4 + - - +
281A LEU* 3.6 2.1 + - - -
283A ALA* 1.3 82.8 - - - +
285A GLN* 1.3 82.1 + - - +
286A GLY 3.9 0.2 - - - -
287A ASN* 5.4 0.4 - - - -
288A MET* 4.2 2.1 - - - +
600A HEM 3.3 72.5 - - + +
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Residues in contact with GLN 285 (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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169A TYR* 3.5 16.7 - - - -
173A LEU* 3.7 34.7 + - + +
176A GLY* 3.3 35.0 - - - -
177A TYR* 3.9 1.4 - - - +
180A LEU* 3.5 19.8 - - - +
181A TYR* 5.3 0.4 - - - -
207A PHE* 5.1 0.4 - - + -
281A LEU* 3.0 35.5 + - + +
284A THR* 1.3 103.0 + - - +
286A GLY* 1.3 56.4 + - - +
287A ASN 3.2 10.8 + - - -
288A MET* 3.4 26.5 + - - +
289A GLY 4.3 2.8 + - - -
446A TYR* 4.8 0.6 + - - -
600A HEM 4.7 1.2 - - - +
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Residues in contact with GLY 286 (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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169A TYR* 3.4 22.1 + - - -
207A PHE* 4.4 2.5 - - - -
211A ASP* 5.0 1.1 - - - +
281A LEU 4.1 0.4 + - - -
282A TRP* 2.8 42.1 + - - +
283A ALA 4.7 0.2 - - - -
285A GLN* 1.3 70.9 - - - +
287A ASN* 1.3 65.7 + - - +
290A PRO* 3.7 12.3 - - - +
485A LEU* 5.0 1.9 - - - +
487A GLN* 4.4 4.7 - - - +
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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