Contacts of the helix formed by residues 164 - 182 (chain B) 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 LEU 164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B MET 3.6 1.2 + - - -
163B GLY* 1.3 71.6 - - - -
165B LEU* 1.3 57.4 + - - +
167B PHE* 3.4 16.6 + - + -
168B SER* 2.8 46.3 + - - +
293B PHE* 3.7 17.5 - - + +
296B LEU* 4.1 14.4 - - + -
297B LEU* 3.8 44.9 - - + +
300B LEU* 3.9 14.4 - - + -
464B LEU* 4.2 11.9 - - + -
491B ASP* 3.1 0.6 + - - -
492B VAL* 2.7 20.8 + - + +
494B VAL* 3.9 20.0 - - + -
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU* 1.3 71.3 - - - +
166B ASP* 1.3 56.2 + - - +
169B TYR* 2.7 53.2 + - + +
208B ARG* 3.9 26.7 - - - +
289B GLY 4.3 1.3 - - - +
290B PRO* 3.9 21.8 - - + -
293B PHE* 3.4 36.7 - - + -
487B GLN* 4.7 7.2 - - + +
488B PRO* 3.7 26.2 - - + +
491B ASP* 2.8 26.8 + - + +
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Residues in contact with ASP 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B MET* 3.5 22.0 - - + +
163B GLY* 3.2 13.7 + - - +
165B LEU* 1.3 76.6 - - - +
167B PHE* 1.3 56.8 + - - +
169B TYR* 4.8 2.0 - - - -
170B SER* 2.6 40.6 + - - -
204B PHE* 4.3 17.7 - - - -
205B HIS* 4.8 8.1 - - - -
491B ASP* 3.2 10.5 + - - +
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Residues in contact with PHE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 4.4 5.8 - - + -
162B MET* 3.7 19.0 - - + +
163B GLY 2.8 18.1 + - - +
164B LEU* 3.5 16.6 - - + +
166B ASP* 1.3 76.1 - - - +
168B SER* 1.3 72.9 + - - +
170B SER* 3.1 7.0 + - - -
171B PHE* 3.0 45.7 + + - -
296B LEU* 4.6 1.3 - - + -
454B PHE* 3.7 19.1 - + - -
458B VAL* 3.9 29.4 - - + -
462B LEU* 4.0 13.9 - - + -
464B LEU* 4.3 13.9 - - + -
494B VAL* 4.8 2.0 - - + -
496B TYR* 3.7 40.2 - + + -
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Residues in contact with SER 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU* 2.8 30.3 + - - +
165B LEU 4.0 1.3 - - - -
167B PHE* 1.3 73.1 - - - +
169B TYR* 1.3 63.1 + - - +
171B PHE* 4.3 0.2 - - - -
172B LEU* 3.2 30.1 + - - +
289B GLY 3.5 19.5 - - - -
292B ALA* 4.3 7.2 - - - -
293B PHE* 3.7 17.0 - - - -
296B LEU* 3.6 21.7 - - - +
454B PHE* 4.0 11.5 - - - -
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Residues in contact with TYR 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 2.7 36.6 + - + +
168B SER* 1.3 74.7 - - - +
170B SER* 1.3 63.6 + - - +
173B LEU* 3.1 37.0 + - + +
204B PHE* 3.6 17.3 - + + -
207B PHE* 3.3 24.5 - + - -
208B ARG* 3.5 39.9 - - - -
211B ASP* 3.0 19.1 + - - -
285B GLN 3.5 19.5 - - - -
286B GLY* 3.5 15.2 + - - -
289B GLY* 3.8 9.1 + - - -
290B PRO* 3.7 31.2 - - + -
487B GLN* 3.9 2.4 + - - -
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Residues in contact with SER 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B MET* 3.9 8.0 - - - +
166B ASP* 2.6 29.0 + - - -
167B PHE* 3.1 7.3 + - - -
169B TYR* 1.3 78.4 - - - +
171B PHE* 1.3 68.6 + - - +
174B ARG* 3.1 49.2 + - - +
204B PHE* 3.6 31.1 - - - -
205B HIS* 6.0 0.9 - - - -
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Residues in contact with PHE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 3.9 6.0 - - + +
147B VAL* 3.6 22.1 - - + +
148B LEU* 3.5 43.7 - - + -
151B ASP* 3.8 29.2 - - + -
162B MET* 4.6 8.7 - - + -
167B PHE* 3.0 55.4 + + - +
170B SER* 1.3 83.8 + - - +
172B LEU* 1.3 61.8 + - - +
174B ARG* 3.8 9.4 - - - +
175B ALA* 3.1 27.0 + - - +
454B PHE* 3.8 18.8 - + + -
496B TYR* 4.3 9.2 - - - -
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B MET* 3.6 16.9 - - + +
144B LEU* 4.0 9.9 - - + -
168B SER 3.2 16.5 + - - +
171B PHE* 1.3 76.7 - - - +
173B LEU* 1.3 57.0 + - - +
176B GLY* 2.8 27.4 + - - -
285B GLN* 3.9 2.5 - - - +
288B MET* 3.5 27.4 - - + +
289B GLY* 3.9 10.8 - - - +
292B ALA* 3.3 33.9 - - + -
450B SER* 3.8 28.9 - - - +
451B ILE* 4.6 4.5 - - + -
454B PHE* 3.8 23.3 - - + -
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B TYR* 3.1 31.4 + - + +
172B LEU* 1.3 74.1 - - - +
174B ARG* 1.3 65.6 + - - +
177B TYR* 2.8 37.0 + - + +
200B SER 4.9 0.4 - - - +
203B VAL* 4.4 13.9 - - + -
204B PHE* 3.9 35.2 - - + +
207B PHE* 3.3 43.1 - - + -
281B LEU* 5.2 2.5 - - + -
285B GLN* 3.7 32.4 - - + +
288B MET* 6.0 0.2 - - - +
289B GLY 5.7 0.2 - - - +
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Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B VAL* 3.4 25.2 - - + +
151B ASP* 2.8 40.6 + - - -
170B SER* 3.1 35.4 + - - +
171B PHE* 3.8 10.7 - - - +
173B LEU* 1.3 79.5 - - - +
175B ALA* 1.3 61.7 + - - +
177B TYR* 3.5 3.7 + - - +
178B LEU* 3.1 30.0 + - - +
197B ARG* 2.8 33.4 + - - +
200B SER* 3.0 41.9 + - - +
201B ALA* 3.5 21.6 - - - +
204B PHE* 3.9 11.7 - - + -
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B MET* 3.6 4.5 - - + -
143B ASN* 3.7 11.7 - - + +
144B LEU* 3.6 47.1 - - + +
147B VAL* 4.4 5.7 - - + +
171B PHE 3.1 19.3 + - - +
174B ARG* 1.3 74.4 - - - +
176B GLY* 1.3 56.8 + - - +
178B LEU* 3.5 0.6 + - - -
179B THR* 2.6 38.3 + - - -
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Residues in contact with GLY 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B MET* 3.5 15.9 - - - +
172B LEU 2.8 17.5 + - - -
175B ALA* 1.3 73.8 - - - +
177B TYR* 1.3 60.6 + - - +
179B THR* 3.3 0.7 + - - -
180B LEU* 2.9 35.7 + - - +
285B GLN* 3.6 17.0 - - - -
288B MET* 4.8 0.4 - - - -
446B TYR* 3.7 7.4 - - - -
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Residues in contact with TYR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B LEU* 2.8 22.9 + - + +
174B ARG* 3.6 4.3 - - - +
176B GLY* 1.3 75.9 - - - +
178B LEU* 1.3 67.1 + - + +
181B TYR* 2.8 76.4 + + + +
199B HIS* 2.6 45.2 + + - -
200B SER* 4.3 12.8 - - - -
203B VAL* 4.0 16.4 - - + -
240B LEU 4.5 1.2 + - - -
241B LEU* 3.9 25.3 - - + +
246B LEU* 4.3 7.7 - - + +
249B ARG* 4.1 18.0 + - - -
281B LEU* 4.1 17.9 - - + -
285B GLN* 4.0 4.2 + - - +
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASN* 3.7 27.8 + - + +
146B ALA* 6.4 0.4 - - + -
147B VAL* 3.9 23.8 - - + -
174B ARG 3.1 19.2 + - - +
175B ALA 3.9 0.9 - - - +
177B TYR* 1.3 91.1 - - + +
179B THR* 1.3 58.0 + - - +
182B GLY* 2.9 34.8 + - - +
183B ILE* 4.0 5.8 - - + +
196B ASP* 3.6 46.0 - - + +
199B HIS* 5.1 0.7 - - + -
200B SER* 4.2 2.5 - - - -
249B ARG* 3.4 28.3 - - - +
251B HIS 4.8 1.0 - - - +
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Residues in contact with THR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B LEU* 3.6 39.1 - - + +
139B ALA* 4.0 9.7 - - + +
140B MET* 3.4 17.5 - - - +
143B ASN* 2.9 18.2 + - - +
175B ALA 2.6 22.3 + - - -
176B GLY 3.6 4.3 - - - -
177B TYR 3.2 0.2 - - - -
178B LEU* 1.3 80.2 - - - +
180B LEU* 1.3 62.0 + - - +
251B HIS 4.1 6.8 - - - +
253B SER* 3.8 15.2 + - - -
446B TYR* 3.7 19.1 - - + +
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 5.0 2.5 - - + -
136B LEU* 3.7 30.3 - - + -
176B GLY 2.9 14.4 + - - +
179B THR* 1.3 76.9 - - - +
181B TYR* 1.3 70.9 + - + +
182B GLY 3.5 0.2 - - - -
253B SER* 2.7 33.3 + - - +
255B TRP* 3.9 28.3 - - + -
256B LEU* 3.4 10.3 - - - +
284B THR* 3.4 40.8 - - + +
285B GLN* 3.5 8.5 - - - +
446B TYR* 4.2 19.3 - - + +
600B HEM 4.6 5.4 - - + -
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Residues in contact with TYR 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B TYR* 2.8 48.9 + + + +
180B LEU* 1.3 86.6 - - + +
182B GLY* 1.3 59.2 + - - +
241B LEU* 3.8 20.0 - - + -
246B LEU* 3.9 28.8 - - + +
249B ARG* 3.4 22.2 + - - +
252B ARG* 4.1 7.7 - - - +
255B TRP* 3.7 23.6 - + - -
256B LEU* 3.9 15.2 - - + +
277B LEU* 2.7 42.4 + - + -
280B GLN* 3.6 4.5 - - - +
281B LEU* 3.1 32.7 + - + -
284B THR* 4.8 0.7 - - + -
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Residues in contact with GLY 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B TYR* 4.4 0.3 - - - +
178B LEU* 2.9 31.4 + - - +
179B THR 4.2 0.6 + - - -
180B LEU 3.5 2.8 + - - -
181B TYR* 1.3 81.1 - - - +
183B ILE* 1.3 54.1 + - - -
249B ARG* 2.9 28.7 + - - -
250B ALA 3.3 12.1 - - - -
251B HIS 3.9 11.9 - - - -
252B ARG* 4.1 2.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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