Contacts of the helix formed by residues 169 - 178 (chain B) in PDB entry 2JDQ
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 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B VAL* 4.2 0.2 - - - -
165B VAL 3.4 0.4 + - - -
166B ILE 3.3 10.9 + - - -
167B GLN 3.1 4.9 - - - -
168B ALA* 1.3 80.4 - - - +
170B ALA* 1.3 61.4 + - - +
171B VAL 3.5 2.4 + - - -
172B PRO* 3.9 14.4 - - - +
173B ILE* 3.2 23.9 - - - +
206B TYR* 5.2 2.2 - - - -
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Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 4.0 24.2 - - + -
135B LEU* 4.5 3.3 - - + +
151B LEU* 5.1 0.9 - - + -
165B VAL* 3.4 38.4 + - + +
166B ILE 4.5 1.4 + - - -
169B GLY* 1.3 76.3 - - - +
171B VAL* 1.3 59.3 + - - +
173B ILE* 3.3 4.6 + - - +
174B PHE* 2.9 47.0 + - + -
196B ILE* 5.2 0.7 - - + -
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ILE* 4.8 6.0 - - + +
170B ALA* 1.3 76.5 - - + +
172B PRO* 1.3 72.8 - - + +
173B ILE 3.2 0.3 + - - -
174B PHE* 3.3 4.1 + - - +
175B ILE* 3.0 42.3 + - + +
193B LEU* 4.2 8.7 - - + -
196B ILE* 3.6 38.6 - - + -
206B TYR* 3.8 23.1 + - + -
207B VAL* 4.0 16.8 - - + -
210B CYS* 3.7 17.0 - - + -
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Residues in contact with PRO 172 (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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169B GLY* 3.9 12.1 - - - +
170B ALA 3.9 1.1 - - - -
171B VAL* 1.3 99.9 - - + +
173B ILE* 1.3 63.0 + - + +
175B ILE* 3.4 9.3 + - + +
176B GLU* 3.2 34.4 + - - +
206B TYR* 3.8 15.0 - - - +
210B CYS* 4.6 11.4 - - + -
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Residues in contact with ILE 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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132B VAL* 3.2 27.4 - - + +
135B LEU* 3.4 39.9 - - + +
136B LYS* 4.1 31.9 - - + -
169B GLY 3.2 22.7 - - - +
170B ALA 3.3 5.1 + - - +
171B VAL 3.2 0.8 - - - -
172B PRO* 1.3 75.0 - - + +
174B PHE* 1.3 67.6 + - - +
176B GLU* 3.2 18.3 + - + +
177B LEU* 3.0 23.3 + - + +
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Residues in contact with PHE 174 (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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135B LEU* 3.7 28.9 - - + -
148B ALA* 4.0 16.2 - - + -
151B LEU* 3.9 24.5 - - + -
165B VAL* 4.8 2.0 - - + -
170B ALA* 2.9 41.3 + - + +
171B VAL 3.6 4.9 - - - +
173B ILE* 1.3 76.6 - - - +
175B ILE* 1.3 55.3 - - - +
177B LEU* 3.3 10.5 + - + +
178B LEU* 3.1 28.1 + - - +
189B ALA* 3.6 23.8 - - + +
192B ALA* 3.6 28.0 - - + -
193B LEU* 3.7 17.9 - - + +
196B ILE* 4.3 16.4 - - + -
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Residues in contact with ILE 175 (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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171B VAL* 3.0 29.0 + - + +
172B PRO* 3.7 7.2 - - + +
173B ILE 3.1 0.2 - - - -
174B PHE* 1.3 74.6 - - - +
176B GLU* 1.3 66.5 + - + +
178B LEU* 3.4 20.5 + - - +
179B SER* 4.3 2.9 + - - -
193B LEU* 4.0 17.0 - - + -
207B VAL* 4.1 1.6 - - + +
210B CYS* 3.4 40.8 - - + +
211B ASN 3.9 18.2 - - - +
212B ILE* 4.0 22.2 - - + -
215B PRO* 4.1 16.8 - - + +
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Residues in contact with GLU 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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172B PRO* 3.2 24.2 + - - +
173B ILE* 3.5 18.0 - - + +
175B ILE* 1.3 77.5 - - + +
177B LEU* 1.3 56.8 + - + +
179B SER* 2.9 29.8 + - - -
180B SER 3.9 1.4 + - - -
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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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135B LEU* 3.9 41.3 - - + +
144B GLN* 3.4 28.7 - - + +
148B ALA* 5.3 2.2 - - + -
173B ILE* 3.0 17.5 + - + +
174B PHE* 3.3 21.7 + - + +
176B GLU* 1.3 73.3 - - + +
178B LEU* 1.3 59.4 + - - +
179B SER 3.0 5.8 - - - -
180B SER* 3.1 27.9 + - - +
185B VAL* 3.4 25.8 - - + -
186B GLN* 3.7 10.7 + - - +
189B ALA* 4.0 11.0 - - + -
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Residues in contact with LEU 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 PHE 3.1 14.7 + - - +
175B ILE* 3.5 14.8 - - - +
176B GLU 3.1 1.0 - - - -
177B LEU* 1.3 76.2 - - - +
179B SER* 1.3 52.7 + - - +
180B SER 3.4 1.1 - - - -
186B GLN* 2.6 39.2 + - - +
189B ALA* 3.9 3.8 - - + -
190B VAL* 3.6 43.1 - - + +
193B LEU* 4.1 7.0 - - + -
212B ILE* 4.1 25.6 - - + +
215B PRO* 4.1 16.6 - - + +
216B LEU* 4.0 26.0 - - + +
219B LEU* 3.8 13.5 - - + +
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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