Contacts of the helix formed by residues 168 - 182 (chain A) in PDB entry 2JJ7
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 ASP 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A SER* 1.3 67.3 + - - +
170A ALA* 3.7 11.6 + - - +
171A ASP* 3.0 44.9 + - + +
172A LEU* 3.0 13.5 + - - +
175A ARG* 5.2 5.8 + - - +
175B ARG* 5.4 8.5 - - - +
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Residues in contact with SER 169 (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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91A THR* 4.3 20.6 + - - -
92A THR* 6.1 0.2 - - - -
95A LYS* 5.2 16.7 - - - +
168A ASP* 1.3 71.9 + - - +
170A ALA* 1.3 58.5 + - - +
172A LEU* 2.9 32.5 + - - +
173A VAL* 3.5 10.7 + - - +
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Residues in contact with ALA 170 (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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168A ASP* 3.3 11.1 + - - +
169A SER* 1.3 80.2 - - - +
171A ASP* 1.3 63.5 + - - +
172A LEU 3.2 0.7 + - - -
173A VAL* 3.9 7.6 + - - +
174A SER* 4.2 11.4 + - - -
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Residues in contact with ASP 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASP* 3.0 33.2 + - + +
170A ALA* 1.3 81.4 - - - +
172A LEU* 1.3 57.3 + - - +
174A SER* 3.8 4.0 + - - -
175A ARG* 3.0 52.9 + - - +
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A THR* 3.6 30.7 - - + -
157A ILE* 4.2 23.3 - - + +
158A VAL* 5.0 1.3 - - + -
163A PHE 6.6 0.4 - - - -
168A ASP 3.0 11.2 + - - +
169A SER* 2.9 19.9 + - - +
171A ASP* 1.3 74.3 - - - +
173A VAL* 1.3 71.2 + - + +
175A ARG* 3.2 10.6 + - - +
176A ILE* 3.0 52.6 + - + +
166B PHE* 4.2 7.6 - - + -
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Residues in contact with VAL 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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84A ARG* 4.1 20.6 - - + +
87A LEU* 4.0 35.3 - - + +
88A THR* 4.2 9.0 - - - +
91A THR* 4.0 19.3 - - - +
169A SER* 3.5 10.0 + - - +
170A ALA 3.9 3.1 + - - +
171A ASP 3.6 0.2 - - - -
172A LEU* 1.3 87.0 - - + +
174A SER* 1.3 58.8 + - - +
176A ILE* 3.3 3.1 + - - +
177A ILE* 3.1 45.8 + - + +
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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
----------------------------------------------------------
84A ARG* 4.6 15.9 + - - +
170A ALA 4.2 9.5 + - - -
171A ASP* 3.8 6.9 + - - -
172A LEU 3.3 0.4 - - - -
173A VAL* 1.3 78.6 - - - +
175A ARG* 1.3 58.0 + - - +
177A ILE* 3.9 7.6 - - - +
178A SER* 2.9 30.3 + - - -
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Residues in contact with ARG 175 (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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168A ASP* 5.2 5.7 + - - +
171A ASP* 3.0 43.7 + - - +
172A LEU* 3.2 5.3 + - - +
174A SER* 1.3 74.3 - - - +
176A ILE* 1.3 65.3 + - - +
178A SER* 3.7 6.5 + - - -
179A ALA* 3.1 22.3 + - - +
165B LYS 4.7 2.9 - - - +
166B PHE* 3.2 64.9 + - + +
167B ILE* 4.1 22.4 - - - +
175B ARG* 5.5 8.9 - - - +
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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
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83A LEU* 5.1 0.2 - - + -
87A LEU* 3.8 21.8 - - + -
153A TRP* 4.3 7.1 - - + -
154A ILE* 4.0 30.5 - - + -
157A ILE* 3.9 23.6 - - + -
158A VAL* 4.2 15.7 - - + -
172A LEU* 3.0 41.4 + - + +
173A VAL 3.6 6.3 - - - +
175A ARG* 1.3 73.5 - - - +
177A ILE* 1.3 65.6 + - - +
179A ALA* 3.1 17.2 + - - +
180A LEU* 3.4 14.1 + - + +
166B PHE* 3.9 17.0 - - + -
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Residues in contact with ILE 177 (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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80A ILE* 4.2 18.2 - - + +
83A LEU* 3.9 18.4 - - + -
84A ARG* 3.8 56.5 - - + +
87A LEU* 4.0 5.2 - - + -
142A PHE* 4.8 4.9 - - + -
173A VAL* 3.1 26.4 + - + +
174A SER* 4.0 4.9 - - - +
176A ILE* 1.3 74.1 - - - +
178A SER* 1.3 58.7 + - - +
180A LEU* 2.9 24.7 + - - +
181A THR* 3.0 30.6 + - + +
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Residues in contact with SER 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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174A SER 2.9 20.7 + - - -
175A ARG* 3.7 8.1 - - - -
177A ILE* 1.3 78.3 - - - +
179A ALA* 1.3 61.4 + - - +
180A LEU 3.2 1.2 + - - -
181A THR* 3.4 15.1 + - - -
182A ASP* 3.0 31.4 + - - +
165B LYS* 4.6 8.4 + - - +
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Residues in contact with ALA 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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153A TRP* 3.8 25.8 - - + -
175A ARG 3.1 13.6 + - - +
176A ILE 3.1 10.9 + - - +
178A SER* 1.3 76.5 + - - +
180A LEU* 1.3 58.7 + - - +
182A ASP* 4.3 1.3 - - - +
160B PHE* 5.2 0.8 - - + -
162B LYS* 3.1 38.6 + - + +
165B LYS* 4.3 19.7 - - + +
166B PHE* 4.3 10.3 - - + +
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Residues in contact with LEU 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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83A LEU* 3.4 33.0 - - + -
133A LEU* 3.8 14.4 - - + -
142A PHE* 3.4 16.1 - - + -
143A HIS* 2.7 33.8 + - - +
144A PHE* 4.2 18.2 - - + -
150A THR* 3.6 29.8 - - + -
153A TRP* 5.0 7.6 - - + -
154A ILE* 4.2 10.8 - - + -
176A ILE* 3.6 17.5 - - + +
177A ILE* 2.9 7.4 + - - +
179A ALA* 1.3 79.9 - - + +
181A THR* 1.3 59.1 + - - +
182A ASP 3.2 5.6 + - - -
160B PHE* 5.1 4.0 - - + -
162B LYS* 4.3 1.6 - - + +
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Residues in contact with THR 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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80A ILE* 4.3 14.8 - - + -
141A VAL 3.4 20.9 - - - +
142A PHE* 4.2 8.7 - - + -
143A HIS* 3.7 9.7 + - - -
177A ILE* 3.0 36.4 + - + +
178A SER* 3.4 13.7 + - - -
180A LEU* 1.3 75.3 - - - +
182A ASP* 1.3 62.9 + - - +
183A LYS* 3.6 3.3 + - - +
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Residues in contact with ASP 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A HIS* 3.4 8.8 - - - +
178A SER* 3.0 31.0 + - - +
179A ALA 4.3 0.2 - - - +
180A LEU 3.2 0.4 - - - -
181A THR* 1.3 77.4 + - - +
183A LYS* 1.3 59.1 + - - +
162B LYS* 2.5 31.1 + - - +
165B LYS* 3.2 43.9 + - + +
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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