Contacts of the helix formed by residues 172 - 190 (chain A) in PDB entry 4IRX
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 172 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A THR 4.4 2.3 + - - -
104A SER* 3.9 5.2 - - - +
126A ARG* 3.1 42.8 - - - +
169A ASP* 3.0 20.0 + - - -
171A GLY* 1.3 78.3 - - - +
173A SER* 1.3 62.1 + - - +
174A SER* 2.6 27.3 + - - -
175A SER* 3.0 13.7 + - - -
176A ILE* 3.2 14.5 + - - +
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Residues in contact with SER 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A SER* 2.8 16.9 + - - -
126A ARG* 3.3 4.7 - - - +
127A ASN* 2.8 57.5 + - - -
137A HIS* 5.1 1.0 + - - -
142A ASN* 5.5 0.5 + - - -
172A SER* 1.3 71.2 + - - +
174A SER* 1.3 59.3 + - - +
176A ILE* 4.4 10.3 - - - +
177A GLU* 2.8 44.4 + - - +
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Residues in contact with SER 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ASP 4.1 9.6 - - - -
126A ARG* 4.3 0.2 - - - -
142A ASN* 3.5 27.8 - - - +
168A ASN* 3.3 7.6 + - - -
172A SER* 2.6 16.1 + - - -
173A SER* 1.3 81.6 + - - +
175A SER* 1.3 56.4 + - - +
178A ARG* 2.9 45.7 + - - +
401A INS 2.6 29.1 + - - -
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Residues in contact with SER 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A THR* 3.9 12.1 - - - -
168A ASN* 2.8 37.0 + - - +
169A ASP 3.1 26.0 + - - -
170A PRO* 4.0 8.3 + - - +
172A SER 3.0 4.3 + - - -
174A SER* 1.3 78.9 + - - +
176A ILE* 1.3 66.1 + - - +
178A ARG* 3.9 0.6 - - - +
179A VAL* 2.9 32.2 + - - +
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Residues in contact with ILE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A SER* 5.9 2.0 - - - -
105A LYS* 6.2 5.6 - - + -
170A PRO 4.0 16.2 - - - +
171A GLY* 4.5 7.0 - - - +
172A SER 3.2 18.9 + - - +
173A SER* 3.8 9.6 - - - +
175A SER* 1.3 77.4 - - - +
177A GLU* 1.3 61.5 + - + +
179A VAL* 3.7 6.3 - - - +
180A LYS* 3.0 27.3 + - + +
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Residues in contact with GLU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASN* 3.5 22.3 + - - -
140A ALA 4.8 2.1 - - - +
142A ASN* 3.7 30.2 + - + +
143A VAL* 3.4 33.0 + - + +
173A SER* 2.8 31.1 + - - +
176A ILE* 1.3 77.1 - - + +
178A ARG* 1.3 65.3 + - - +
180A LYS* 3.2 5.2 + - + +
181A GLY 3.0 18.0 + - - -
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Residues in contact with ARG 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASN* 2.9 46.5 + - - +
146A GLY* 3.4 7.7 - - - +
149A MSE 5.5 0.2 - - - -
168A ASN* 3.8 11.8 - - - +
174A SER* 2.9 24.7 + - - +
175A SER 3.9 0.2 - - - +
177A GLU* 1.3 77.1 - - - +
179A VAL* 1.3 63.0 + - - +
181A GLY 3.3 1.2 + - - -
182A VAL* 3.1 26.5 + - - +
230A LEU* 2.8 58.1 + - + -
257A PHE* 3.4 34.1 - - + -
278A GLN* 3.4 12.9 + - - +
401A INS 2.8 40.0 + - - -
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Residues in contact with VAL 179 (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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165A VAL* 5.0 2.9 - - + -
167A THR* 3.6 32.8 - - + -
175A SER* 2.9 23.1 + - - +
176A ILE* 3.7 6.7 - - - +
178A ARG* 1.3 75.3 - - - +
180A LYS* 1.3 58.5 + - - +
182A VAL* 3.2 6.4 + - - +
183A HIS* 2.9 66.5 + - + +
198A GLU* 3.7 9.9 - - - +
230A LEU* 3.7 10.1 - - + -
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Residues in contact with LYS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A VAL* 4.4 19.1 - - + +
176A ILE* 3.0 19.5 + - + +
177A GLU* 3.2 9.1 + - + +
179A VAL* 1.3 78.1 - - - +
181A GLY* 1.3 56.7 + - - +
183A HIS* 3.3 10.3 + - + +
184A ASP* 2.8 65.6 + - - +
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Residues in contact with GLY 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A VAL* 3.4 26.7 - - - +
147A ARG* 3.3 21.3 - - - -
177A GLU 3.0 11.3 + - - -
178A ARG 3.3 2.6 + - - -
180A LYS* 1.3 75.7 - - - +
182A VAL* 1.3 61.4 + - - +
184A ASP* 3.3 10.9 + - - +
185A GLY 3.1 18.4 + - - -
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLY* 3.5 21.9 - - - +
149A MSE 4.4 10.8 - - - -
150A ALA* 3.3 6.0 - - + +
165A VAL* 4.1 17.7 - - + -
178A ARG 3.1 16.7 + - - +
179A VAL* 3.5 9.9 - - - +
181A GLY* 1.3 72.2 - - - +
183A HIS* 1.3 71.4 + - + +
185A GLY 3.3 1.4 + - - -
186A LEU* 3.0 36.5 + - + +
195A ILE* 5.0 0.2 - - + -
228A LEU* 3.8 31.4 - - + -
230A LEU* 4.7 10.3 - - + -
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Residues in contact with HIS 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A VAL* 2.9 40.8 + - + +
180A LYS* 3.5 9.2 - - + +
182A VAL* 1.3 80.1 - - + +
184A ASP* 1.3 60.4 + - - +
186A LEU* 4.2 0.4 - - - +
187A ALA* 2.8 35.1 + - - +
195A ILE* 3.7 22.8 - - + +
198A GLU* 2.6 35.3 + - - -
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Residues in contact with ASP 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A VAL* 4.0 6.9 - - - +
147A ARG* 3.5 21.8 + - - +
180A LYS* 2.8 59.3 + - - +
181A GLY* 3.5 12.3 - - - +
182A VAL 3.3 0.2 - - - -
183A HIS* 1.3 74.2 - - - +
185A GLY* 1.3 58.5 + - - +
187A ALA* 3.8 4.6 - - - +
188A ALA* 3.0 28.4 + - - +
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Residues in contact with GLY 185 (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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147A ARG* 3.3 27.1 - - - +
150A ALA* 3.6 14.4 - - - -
151A ASP* 4.1 4.3 - - - +
154A VAL* 3.7 11.3 - - - +
181A GLY 3.1 8.3 + - - -
184A ASP* 1.3 79.3 - - - +
186A LEU* 1.3 59.9 + - - +
188A ALA* 3.4 3.8 + - - +
189A GLY 3.1 20.8 + - - -
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Residues in contact with LEU 186 (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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150A ALA* 3.9 24.2 - - + +
153A VAL* 4.2 22.7 - - + -
154A VAL* 4.2 7.2 - - + -
163A VAL* 4.1 21.8 - - + -
182A VAL* 3.0 28.3 + - + +
183A HIS 4.2 1.6 - - - +
185A GLY* 1.3 73.4 - - - +
187A ALA* 1.3 64.2 + - - +
189A GLY* 3.1 2.4 + - - +
190A GLY 3.0 24.8 + - - +
193A PHE* 4.0 21.3 - - + +
195A ILE* 3.7 37.9 - - + -
228A LEU* 4.8 1.3 - - + -
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Residues in contact with ALA 187 (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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183A HIS 2.8 23.4 + - - +
184A ASP* 3.8 5.2 - - - +
186A LEU* 1.3 72.5 - - - +
188A ALA* 1.3 63.6 + - - +
190A GLY* 3.2 15.0 + - - +
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Residues in contact with ALA 188 (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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147A ARG* 3.6 21.5 - - - +
184A ASP 3.0 18.1 + - - +
185A GLY 3.5 6.3 - - - +
186A LEU 3.2 0.2 - - - -
187A ALA* 1.3 79.2 - - - +
189A GLY* 1.3 60.8 + - - +
190A GLY* 3.6 0.3 + - - -
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Residues in contact with GLY 189 (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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154A VAL* 4.2 13.2 - - - +
185A GLY 3.1 13.2 + - - -
186A LEU 3.1 4.8 + - - -
188A ALA* 1.3 78.3 - - - +
190A GLY* 1.3 55.3 + - - +
192A ALA* 5.1 1.6 + - - +
193A PHE* 3.4 33.8 - - - -
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Residues in contact with GLY 190 (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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186A LEU 3.0 9.7 + - - +
187A ALA* 3.2 13.2 + - - -
188A ALA 4.5 0.4 - - - -
189A GLY* 1.3 77.9 - - - +
191A PRO* 1.3 69.0 - - - +
192A ALA 3.1 5.4 - - - -
193A PHE* 2.9 28.1 + - - +
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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