Contacts of the helix formed by residues 177 - 188 (chain A) in PDB entry 2P7I
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 ALA 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A ASN* 3.9 4.9 - - - +
143A ALA* 4.3 6.1 - - + -
144A ASN* 3.7 31.4 - - - +
161A SER* 6.2 1.6 - - - -
175A THR 3.8 1.0 + - - -
176A TYR* 1.3 73.7 - - - +
178A LEU* 1.3 68.2 + - - +
179A ASP* 3.2 19.1 - - - +
180A THR* 2.9 8.3 + - + +
181A LEU* 2.9 23.0 + - - +
234A ASP* 5.0 0.2 - - - +
239A ILE* 3.2 10.5 - - - -
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Residues in contact with LEU 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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142A ASN* 4.6 0.8 + - - -
177A ALA* 1.3 75.0 - - - +
179A ASP* 1.3 62.5 + - - +
181A LEU* 4.2 1.3 - - - +
182A GLU* 3.1 27.2 + - - +
195A ARG* 4.2 6.1 - - + -
196A SER 4.2 9.0 - - - +
233A PRO* 4.1 7.9 - - + -
234A ASP* 4.0 39.7 + - + +
239A ILE* 3.3 29.6 - - + +
241A LEU* 3.9 26.0 - - + +
231B GLN* 3.5 46.9 + - + +
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Residues in contact with ASP 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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144A ASN* 5.4 0.3 + - - -
177A ALA* 3.4 20.1 - - - +
178A LEU* 1.3 77.8 - - - +
180A THR* 1.3 75.0 + - - +
182A GLU* 4.0 2.0 - - - +
183A ARG* 3.0 28.1 + - - +
231B GLN* 5.3 1.1 + - - +
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Residues in contact with THR 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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161A SER* 6.2 4.0 - - - -
174A CYS* 5.5 2.9 - - - -
175A THR 4.6 1.2 + - - -
176A TYR* 3.5 13.5 - - - -
177A ALA* 2.9 27.4 + - + +
179A ASP* 1.3 90.0 + - - +
181A LEU* 1.3 63.3 + - - +
183A ARG* 3.5 35.2 + - - +
184A ASP* 3.1 28.9 + - - +
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Residues in contact with LEU 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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112A LEU* 3.8 29.2 - - + -
138A LEU* 3.8 18.2 - - + +
140A CYS* 3.9 21.8 - - + -
176A TYR* 3.5 14.3 - - + -
177A ALA 2.9 17.4 + - - +
178A LEU* 4.2 2.7 - - - +
180A THR* 1.3 79.7 + - - +
182A GLU* 1.3 57.6 + - - +
184A ASP* 3.4 2.3 + - + +
185A ALA* 3.0 27.5 + - - +
239A ILE* 3.7 36.6 - - + +
241A LEU* 3.8 25.1 - - + -
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Residues in contact with GLU 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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178A LEU 3.1 18.1 + - - +
179A ASP* 4.2 2.2 - - - +
181A LEU* 1.3 74.4 - - - +
183A ARG* 1.3 66.3 - - - +
185A ALA* 3.8 0.8 - - - +
186A SER* 2.9 27.7 + - - -
192A VAL* 3.8 18.4 - - + +
195A ARG* 2.8 49.8 + - - +
241A LEU* 3.6 16.0 - - + +
227B GLN* 3.1 13.8 - - - +
231B GLN* 4.1 8.0 + - - -
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Residues in contact with ARG 183 (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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174A CYS* 5.5 4.4 - - - -
176A TYR* 4.8 2.2 - - - -
179A ASP 3.0 19.4 + - - +
180A THR* 3.5 34.7 + - - +
182A GLU* 1.3 76.8 - - - +
184A ASP* 1.3 85.0 + - - +
186A SER* 3.6 4.7 - - - -
187A ARG* 2.9 72.2 + - + +
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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
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118A PRO* 3.7 10.0 - - + +
119A VAL* 3.8 28.5 - - + +
122A LEU* 3.8 12.9 - - + +
174A CYS* 5.5 0.3 - - - -
176A TYR* 2.6 34.7 + - + +
180A THR 3.1 14.0 + - - +
181A LEU 3.9 3.8 - - - +
182A GLU 3.3 0.2 - - - -
183A ARG* 1.3 108.5 + - - +
185A ALA* 1.3 62.7 + - - +
187A ARG* 3.4 5.2 + - - -
188A ALA* 3.1 22.2 + - - +
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Residues in contact with ALA 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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122A LEU* 3.8 10.4 - - - +
138A LEU* 4.3 15.0 - - + -
181A LEU 3.0 17.0 + - - +
182A GLU 3.8 3.8 - - - +
184A ASP* 1.3 76.6 - - - +
186A SER* 1.3 62.8 + - - +
188A ALA* 3.2 9.5 + - - +
190A LEU* 3.1 41.3 + - + +
192A VAL* 3.9 20.0 - - + -
241A LEU* 4.3 1.3 - - + -
243A CYS* 4.3 3.1 - - - -
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Residues in contact with SER 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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182A GLU* 2.9 24.4 + - - -
183A ARG* 3.6 5.4 - - - -
185A ALA* 1.3 75.3 - - - +
187A ARG* 1.3 66.3 + - - +
189A GLY* 3.0 14.7 + - - -
190A LEU 4.1 10.2 + - - +
192A VAL* 4.8 3.3 - - - +
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Residues in contact with ARG 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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119A VAL* 4.0 22.9 - - + +
123A LYS* 5.8 1.2 - - - +
183A ARG* 2.9 59.2 + - + +
184A ASP* 3.8 13.5 + - - +
185A ALA 3.3 0.4 - - - -
186A SER* 1.3 76.0 - - - +
188A ALA* 1.3 59.6 + - - +
189A GLY* 3.2 1.1 + - - -
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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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119A VAL* 3.7 11.9 - - - +
122A LEU* 3.4 35.0 - - + +
123A LYS* 3.5 39.0 + - - +
126A ASN* 3.9 9.2 + - - +
127A ASP* 4.5 0.7 - - - +
184A ASP 3.1 9.5 + - - +
185A ALA 3.4 9.9 - - - +
186A SER 3.1 1.0 - - - -
187A ARG* 1.3 76.2 - - - +
189A GLY* 1.3 58.4 + - - +
190A LEU* 3.5 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
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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