Contacts of the helix formed by residues 172 - 188 (chain B) in PDB entry 2IHM
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 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ALA* 3.0 17.2 + - - +
168B GLY 4.3 0.2 + - - -
170B GLU* 3.7 27.2 + - - +
171B ALA* 1.3 81.2 - - - +
173B GLU* 1.3 58.9 + - - +
174B GLY 3.2 3.1 - - - +
175B ARG* 3.3 45.7 + - + +
176B LEU* 3.0 25.9 + - - +
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Residues in contact with GLU 173 (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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168B GLY* 3.9 22.3 - - - +
171B ALA* 3.6 9.6 + - - +
172B ASN* 1.3 69.4 - - - +
174B GLY* 1.3 60.5 + - - +
175B ARG 3.3 0.2 - - - -
176B LEU* 3.8 26.4 - - - +
177B LEU* 2.9 28.4 + - - +
248B VAL* 5.5 3.1 - - - +
444B ARG* 4.9 10.9 + - - +
4U C 6.6 0.2 - - + -
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Residues in contact with GLY 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ASN* 3.2 1.6 - - - +
173B GLU* 1.3 75.3 - - - +
175B ARG* 1.3 64.3 + - - +
177B LEU* 3.4 3.3 + - - +
178B SER 3.2 12.3 + - - -
1E G 3.1 48.7 + - - +
4U C 3.9 17.0 - - - +
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Residues in contact with ARG 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ALA* 3.7 12.3 - - + -
172B ASN* 3.3 42.9 + - + +
174B GLY* 1.3 75.0 - - - +
176B LEU* 1.3 65.5 + - - +
177B LEU 3.3 0.2 + - - -
178B SER* 3.3 2.1 + - - -
179B PHE* 3.2 33.0 + - + -
1E G 3.0 83.0 + - + +
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Residues in contact with LEU 176 (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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164B ALA* 3.3 31.9 - - + +
165B GLU* 4.9 4.3 - - - -
167B ALA* 3.7 1.7 - - - +
168B GLY* 3.5 25.8 - - - +
172B ASN 3.0 16.8 + - - +
173B GLU* 3.8 25.4 - - - +
174B GLY 3.3 0.2 - - - -
175B ARG* 1.3 76.9 - - - +
177B LEU* 1.3 66.4 + - - +
180B SER* 2.9 39.5 + - - +
440B GLN* 6.2 0.4 - - - +
444B ARG* 4.4 15.0 - - - +
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Residues in contact with LEU 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 GLU 2.9 19.0 + - - +
174B GLY 3.6 5.8 - - - +
175B ARG 3.1 0.2 - - - -
176B LEU* 1.3 82.1 - - - +
178B SER* 1.3 56.8 + - - +
180B SER* 3.3 5.0 - - - -
181B ARG* 2.9 58.8 + - - +
441B PHE* 4.0 22.4 - - + -
444B ARG* 3.4 30.5 - - - +
445B GLU* 5.1 0.7 - - - +
1E G 4.9 0.4 - - - +
4U C 3.6 41.5 - - + +
5U A 4.0 3.8 - - - +
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Residues in contact with SER 178 (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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174B GLY 3.2 3.6 + - - -
175B ARG 4.0 0.2 - - - -
177B LEU* 1.3 73.8 - - - +
179B PHE* 1.3 68.2 + - - +
180B SER 3.1 1.3 - - - -
181B ARG* 3.1 12.5 + - - +
182B ALA* 2.9 24.6 + - - +
204B TYR* 4.6 5.3 - - - +
209B SER* 5.4 0.7 - - - -
1E G 2.6 57.8 + - - -
2E C 3.3 21.3 + - - -
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Residues in contact with PHE 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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160B LEU* 3.6 31.4 - - + +
163B LEU* 3.8 45.5 - - + -
164B ALA* 3.6 13.2 - - + -
167B ALA* 4.6 2.7 - - + -
175B ARG* 3.2 27.2 + - + +
178B SER* 1.3 77.6 - - - +
180B SER* 1.3 58.8 + - - +
182B ALA* 3.3 5.0 + - - +
183B ALA* 2.8 30.8 + - - +
208B HIS* 4.0 26.2 - + - -
209B SER* 3.8 20.9 - - - -
1E G 3.6 35.9 - - - -
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Residues in contact with SER 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLU* 6.0 0.9 - - - -
164B ALA* 3.9 10.4 - - - +
176B LEU* 2.9 33.3 + - - +
177B LEU* 3.3 9.6 - - - -
179B PHE* 1.3 77.4 - - - +
181B ARG* 1.3 62.9 + - - +
183B ALA* 3.2 7.7 + - - +
184B SER* 2.9 24.3 + - - -
441B PHE* 4.3 20.6 - - - -
444B ARG* 6.4 0.2 - - - -
496B ALA* 5.1 0.9 - - - +
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Residues in contact with ARG 181 (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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145B ARG* 4.5 1.0 + - - -
177B LEU* 2.9 48.6 + - - +
178B SER* 3.1 12.1 + - - +
180B SER* 1.3 75.0 - - - +
182B ALA* 1.3 62.9 + - - +
184B SER* 3.2 4.7 + - - -
185B VAL* 3.1 24.8 + - - +
204B TYR* 3.5 54.3 + - + -
441B PHE* 3.4 24.5 - - + -
445B GLU* 3.3 16.0 + - - +
448B ARG* 3.4 36.6 - - - +
1E G 4.5 12.3 + - - -
2E C 5.3 3.0 + - - -
3U G 5.4 2.6 - - - +
4U C 4.1 10.7 + - - -
5U A 4.7 0.4 + - - -
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Residues in contact with ALA 182 (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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160B LEU* 4.0 12.3 - - + -
178B SER 2.9 13.4 + - - +
179B PHE 3.6 4.9 - - - +
181B ARG* 1.3 77.6 - - - +
183B ALA* 1.3 60.1 + - - +
185B VAL* 3.2 14.1 + - - +
186B LEU* 3.4 16.5 + - - +
204B TYR* 3.5 27.3 - - - +
205B PHE* 3.6 14.5 - - + -
209B SER* 3.9 17.0 - - - +
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Residues in contact with ALA 183 (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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157B SER* 3.3 18.4 + - - +
160B LEU* 4.0 17.7 - - + +
161B GLU* 3.8 33.2 - - + +
179B PHE 2.8 21.5 + - - +
180B SER* 3.2 8.3 + - - +
182B ALA* 1.3 73.7 - - - +
184B SER* 1.3 60.7 + - - +
186B LEU* 3.6 4.5 + - - +
187B LYS* 3.3 19.6 + - - +
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Residues in contact with SER 184 (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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142B ALA* 4.0 0.2 - - - +
145B ARG* 3.0 17.3 + - - -
147B SER* 4.8 1.7 + - - -
180B SER 2.9 12.2 + - - -
181B ARG 3.5 9.0 - - - -
182B ALA 3.1 0.2 - - - -
183B ALA* 1.3 76.2 - - - +
185B VAL* 1.3 68.8 + - - +
187B LYS* 3.2 7.6 + - - +
188B SER* 3.2 19.6 + - - -
441B PHE* 3.5 18.3 - - - -
496B ALA* 3.3 37.6 + - - +
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Residues in contact with VAL 185 (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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138B MET* 3.8 14.2 - - + +
145B ARG* 4.0 17.5 - - - +
181B ARG 3.1 15.6 + - - +
182B ALA 3.2 8.3 + - - +
184B SER* 1.3 75.4 - - - +
186B LEU* 1.3 65.3 + - - +
188B SER* 2.9 21.5 + - - -
189B LEU* 3.4 6.0 + - + +
202B LEU* 3.7 26.9 - - + -
203B PRO* 3.5 33.2 - - + +
204B TYR* 4.7 3.6 - - + -
205B PHE* 3.5 20.4 - - + -
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Residues in contact with LEU 186 (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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151B HIS* 4.3 1.7 + - - +
153B ASN* 3.7 22.1 + - + +
156B LEU* 3.9 28.0 - - + -
157B SER* 3.9 13.9 - - - +
160B LEU* 3.8 27.4 - - + -
182B ALA 3.4 9.4 + - - +
183B ALA* 3.6 6.3 - - - +
184B SER 3.2 0.2 - - - -
185B VAL* 1.3 77.3 - - - +
187B LYS* 1.3 61.6 + - - +
188B SER 3.0 1.4 + - - -
189B LEU* 3.1 37.8 + - + +
193B VAL* 4.3 13.7 - - + -
199B LEU* 4.5 5.6 - - + -
205B PHE* 3.5 20.2 - - + -
213B ILE* 4.1 6.3 - - + -
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Residues in contact with LYS 187 (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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147B SER* 5.3 5.8 - - - -
148B PRO* 4.1 12.9 - - - +
151B HIS* 3.2 53.2 - - + +
157B SER* 3.5 13.0 - - - +
161B GLU* 3.0 31.3 + - - -
183B ALA* 3.3 15.7 + - - +
184B SER* 3.2 10.1 + - - +
186B LEU* 1.3 79.1 - - - +
188B SER* 1.3 59.5 + - - +
189B LEU 3.5 0.6 - - - +
495B ASN 3.7 18.7 + - - +
496B ALA* 3.2 33.1 + - - +
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Residues in contact with SER 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B MET* 3.4 16.1 - - - +
145B ARG* 3.4 27.8 + - - -
146B PRO* 3.1 28.4 - - - +
147B SER* 4.5 3.6 - - - -
148B PRO* 5.0 2.7 - - - -
184B SER 3.2 6.7 + - - -
185B VAL 2.9 14.4 + - - -
187B LYS* 1.3 78.1 - - - +
189B LEU* 1.3 62.0 + - - +
190B PRO* 3.7 4.5 - - - +
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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