Contacts of the helix formed by residues 172 - 183 (chain A) in PDB entry 2IPX
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 GLY 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A VAL* 4.5 2.9 - - - +
169A ALA 3.0 15.5 + - - -
170A ALA* 3.3 0.4 - - - +
171A SER* 1.3 79.6 - - - +
173A THR* 1.3 57.2 + - - +
174A THR 3.6 1.1 - - - -
175A VAL* 3.8 9.2 - - - -
176A SER* 2.7 35.2 + - - -
201A LEU* 3.6 14.1 - - - -
204A LEU* 3.7 9.1 - - - +
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Residues in contact with THR 173 (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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118A VAL* 5.0 1.1 - - + -
119A TYR* 3.6 46.1 - - + -
142A ARG* 4.3 23.6 + - - +
143A SER* 6.1 0.2 - - - -
169A ALA 4.7 0.8 + - - -
170A ALA* 6.0 0.4 - - - +
171A SER* 5.1 10.8 - - - +
172A GLY* 1.3 76.7 - - - +
174A THR* 1.3 70.0 + - - +
176A SER* 2.6 22.9 + - - -
177A HIS* 3.2 12.0 - - - -
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Residues in contact with THR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A TRP* 4.6 3.1 - - + -
142A ARG 4.6 1.6 + - - -
143A SER* 2.9 38.7 + - - +
144A LYS 4.5 1.4 + - - -
145A LEU* 4.1 19.5 - - + +
166A TYR* 3.3 31.6 + - + +
169A ALA 5.8 0.2 + - - -
173A THR* 1.3 81.5 + - - +
175A VAL* 1.3 66.6 - - - +
177A HIS* 2.9 11.0 + - - +
178A VAL* 2.9 26.0 + - + +
235A PHE* 5.0 0.9 - - + -
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A TYR* 3.6 37.2 - - + -
169A ALA* 3.7 27.1 + - + +
172A GLY* 3.5 13.1 + - - +
173A THR 3.3 0.2 - - - -
174A THR* 1.3 78.1 - - - +
176A SER* 1.3 56.4 + - - +
178A VAL* 3.2 7.9 + - - +
179A SER* 2.8 27.7 + - - -
188A VAL* 3.9 15.9 - - + -
190A ALA* 4.3 10.8 - - + -
201A LEU* 4.8 1.1 - - + -
204A LEU* 4.6 3.4 - - + -
211A ILE* 3.8 24.5 - - + -
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Residues in contact with SER 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 3.8 24.0 - - - -
119A TYR* 3.9 4.2 - - - -
136A ARG* 3.0 32.6 + - - -
172A GLY 2.7 19.2 + - - -
173A THR 2.6 19.6 + - - -
175A VAL* 1.3 74.6 - - - +
177A HIS* 1.3 55.6 + - - +
179A SER* 3.4 5.1 + - - -
180A ASP 3.0 21.1 + - - -
204A LEU* 4.2 8.7 - - - -
208A ARG* 3.2 11.3 + - - +
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Residues in contact with HIS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A THR* 2.9 24.4 + - + +
119A TYR* 2.6 29.0 + - - -
136A ARG* 3.3 22.3 + - - +
137A ALA 3.1 24.5 - - - -
138A TRP* 3.3 52.1 - + + +
143A SER* 5.6 0.4 - - - -
173A THR 3.2 25.4 - - - -
174A THR* 2.9 7.2 + - - +
176A SER* 1.3 73.2 + - - +
178A VAL* 1.3 68.3 + - - +
180A ASP* 3.3 3.2 + - - +
181A ILE* 3.0 29.3 + - - +
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Residues in contact with VAL 178 (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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145A LEU* 3.8 28.7 - - + -
158A ILE* 3.8 21.8 - - + -
164A VAL* 4.3 14.8 - - + -
166A TYR* 4.1 18.6 - - + -
174A THR* 2.9 17.2 + - + +
175A VAL* 3.6 9.2 - - - +
177A HIS* 1.3 76.1 - - - +
179A SER* 1.3 55.9 + - - +
181A ILE* 3.1 8.9 + - - +
182A VAL* 2.9 31.3 + - + +
188A VAL* 3.5 25.4 - - + -
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Residues in contact with SER 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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112A LEU* 3.6 5.0 - - - +
175A VAL 2.8 20.2 + - - -
176A SER 3.4 6.3 - - - -
178A VAL* 1.3 71.9 - - - +
180A ASP* 1.3 61.5 + - - +
182A VAL* 3.5 0.4 - - - +
183A GLY* 3.0 10.4 + - - -
188A VAL* 3.6 11.0 - - - +
208A ARG* 3.0 19.9 + - - -
210A ASN* 2.5 47.8 + - - +
211A ILE* 3.8 18.2 - - - -
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Residues in contact with ASP 180 (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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96A GLY 5.4 0.4 - - - -
109A THR* 2.7 30.0 + - - +
110A LYS* 3.0 29.1 + - - +
112A LEU* 3.0 22.5 + - - +
136A ARG* 3.0 21.8 + - - -
176A SER 3.0 15.2 + - - -
177A HIS 3.3 8.5 + - - +
179A SER* 1.3 75.8 - - - +
181A ILE* 1.3 64.7 + - - +
183A GLY* 3.3 10.7 + - - -
208A ARG* 2.8 25.9 + - - +
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Residues in contact with ILE 181 (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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95A GLU 3.9 12.3 - - - +
96A GLY* 3.7 22.4 - - - +
97A VAL* 3.9 11.0 - - + -
109A THR* 3.8 7.2 - - + -
138A TRP* 3.7 34.1 - - + -
145A LEU* 5.1 2.2 - - + -
156A ILE* 4.8 5.6 - - + -
158A ILE* 3.6 36.6 - - + +
159A LYS* 3.7 11.7 - - - -
160A PRO* 3.4 20.1 - - - +
177A HIS 3.0 21.0 + - - +
178A VAL* 3.5 7.0 - - - +
180A ASP* 1.3 80.7 - - - +
182A VAL* 1.3 63.0 + - - +
183A GLY* 4.3 0.7 - - - -
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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
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158A ILE* 3.9 11.2 - - + -
159A LYS 3.6 17.0 - - - +
160A PRO* 3.6 2.0 - - - +
161A GLY* 2.8 22.7 + - - -
162A ALA* 3.6 23.1 - - + +
164A VAL* 3.8 23.1 - - + -
178A VAL* 2.9 23.6 + - + +
179A SER 3.5 0.4 - - - +
181A ILE* 1.3 75.7 - - - +
183A GLY* 1.3 66.0 + - - +
184A PRO* 4.7 0.2 - - - +
185A ASP 4.3 0.7 + - - -
186A GLY* 3.4 4.8 + - - -
187A LEU 3.9 12.6 - - - +
188A VAL* 3.8 15.5 - - + -
210A ASN* 3.5 18.4 - - - +
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Residues in contact with GLY 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 3.9 7.4 - - - -
160A PRO* 5.6 0.9 - - - -
179A SER 3.0 13.0 + - - -
180A ASP 3.7 11.0 - - - -
181A ILE 3.2 2.7 - - - -
182A VAL* 1.3 77.1 - - - +
184A PRO* 1.4 76.0 - - - +
186A GLY 3.1 11.8 + - - +
210A ASN* 2.9 19.1 + - - -
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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
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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