Contacts of the helix formed by residues 172 - 184 (chain B) in PDB entry 5GJQ
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 GLN 172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B ASN* 5.4 0.3 - - - +
153B LYS* 3.6 21.7 - - - +
167B ALA* 3.6 22.1 + - - +
168B ALA* 4.3 3.2 - - - +
169B GLY 3.4 27.7 + - - +
170B VAL 2.8 8.8 + - - +
171B LYS* 1.3 70.9 - - - +
173B THR* 1.3 69.4 + - + +
174B GLU* 3.2 1.3 + - - -
175B SER* 3.1 4.9 + - - -
176B THR* 2.8 42.2 + - + +
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Residues in contact with THR 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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170B VAL 4.6 2.2 + - - +
172B GLN* 1.3 83.0 + - + +
174B GLU* 1.3 78.5 + - - +
176B THR* 2.2 27.5 + - - -
177B SER* 2.9 19.9 + - - -
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Residues in contact with GLU 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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170B VAL 4.0 2.6 - - - +
171B LYS* 3.4 37.4 + - + +
172B GLN 3.5 0.3 + - - -
173B THR* 1.3 88.2 + - - +
175B SER* 1.3 60.5 + - - +
177B SER* 3.2 8.7 + - - -
178B PHE* 2.9 29.2 + - - +
205B VAL* 3.9 19.7 - - + +
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Residues in contact with SER 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 3.9 7.2 - - - +
167B ALA* 3.5 21.1 - - - +
171B LYS 3.2 22.0 + - - -
172B GLN 3.1 4.8 + - - -
174B GLU* 1.3 78.3 - - - +
176B THR* 1.3 57.3 + - - +
178B PHE* 3.5 1.8 - - - +
179B LEU* 2.9 38.2 + - - +
201B CYS* 2.6 33.8 - - - -
205B VAL* 4.5 8.7 - - - +
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Residues in contact with THR 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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166B THR* 5.3 4.0 - - + -
167B ALA 4.9 11.9 - - - +
172B GLN* 2.8 26.9 + - + +
173B THR* 2.2 37.2 + - - -
175B SER* 1.3 73.8 - - - +
177B SER* 1.3 57.7 + - - -
179B LEU* 3.4 2.7 + - - +
180B GLU* 2.8 38.3 + - - +
55C LEU* 3.9 25.5 - - + +
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Residues in contact with SER 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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173B THR 2.9 15.9 + - - -
174B GLU* 3.4 11.4 - - - -
176B THR* 1.3 77.6 + - - +
178B PHE* 1.3 62.5 + - - +
180B GLU* 3.1 20.8 + - - +
181B LYS* 3.0 23.6 + - - +
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Residues in contact with PHE 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 GLU 2.9 16.4 + - - +
175B SER* 3.5 6.5 - - - +
177B SER* 1.3 76.8 - - - +
179B LEU* 1.3 70.3 + - + +
181B LYS* 3.1 9.2 + - - +
182B LYS* 3.0 51.1 + - + +
197B THR 4.0 4.3 - - - -
200B THR* 4.1 10.1 - - - -
201B CYS* 3.5 43.5 - - + +
204B THR* 3.6 29.2 - - + +
205B VAL* 6.4 0.7 - - + -
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Residues in contact with LEU 179 (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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40B VAL* 4.0 13.5 - - + -
42B VAL* 4.1 20.2 - - + -
165B ALA* 4.0 17.9 - - + -
166B THR* 3.8 27.6 - - - +
175B SER* 2.9 26.3 + - - +
176B THR* 3.9 3.8 - - - +
178B PHE* 1.3 88.3 - - + +
180B GLU* 1.3 57.9 + - - +
182B LYS* 3.1 3.8 + - + +
183B VAL* 2.9 39.2 + - + +
197B THR* 4.2 15.7 - - + -
201B CYS* 3.7 14.1 - - + -
55C LEU* 4.4 11.7 - - + -
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Residues in contact with GLU 180 (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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176B THR* 2.8 21.5 + - - +
177B SER* 3.1 33.1 + - - +
179B LEU* 1.3 72.9 - - - +
181B LYS* 1.3 60.2 + - + +
183B VAL* 4.1 4.2 - - - +
184B LYS* 3.2 40.6 + - - +
52C LYS 5.0 1.9 - - - +
53C SER* 4.5 17.4 - - - -
54C ILE* 4.9 11.8 + - + +
55C LEU* 4.7 17.9 - - + -
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Residues in contact with LYS 181 (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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177B SER 3.0 13.5 + - - +
178B PHE* 3.1 12.3 + - - +
180B GLU* 1.3 82.2 - - + +
182B LYS* 1.3 61.9 + - + +
183B VAL 3.4 0.5 + - - -
184B LYS* 3.7 16.1 + - - +
185B LYS* 3.9 14.4 - - - +
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Residues in contact with LYS 182 (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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178B PHE* 3.0 33.8 + - + +
179B LEU* 3.1 7.8 + - + +
181B LYS* 1.3 77.0 - - + +
183B VAL* 1.3 63.0 + - + +
184B LYS 3.5 0.2 - - - -
185B LYS* 3.8 24.7 - - + +
186B LYS 5.1 0.2 + - - -
189B TRP* 3.9 13.3 - - + -
193B GLN* 4.6 12.5 - - - +
196B GLU* 4.7 1.8 + - - +
197B THR* 3.7 40.2 + - + +
200B THR* 3.7 22.6 + - - +
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Residues in contact with VAL 183 (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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42B VAL* 6.0 1.1 - - + -
164B LYS* 4.2 29.8 - - + +
165B ALA* 4.7 10.8 - - + -
179B LEU* 2.9 23.7 + - + +
180B GLU* 4.5 6.1 - - - +
181B LYS 3.3 0.2 - - - -
182B LYS* 1.3 78.2 - - - +
184B LYS* 1.3 67.2 + - + +
185B LYS 3.1 3.7 + - - -
186B LYS* 3.3 13.3 + - - +
189B TRP* 4.1 29.4 + - + +
54C ILE* 5.3 10.8 - - + -
55C LEU* 4.6 13.7 - - + -
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Residues in contact with LYS 184 (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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180B GLU* 3.2 31.4 + - - +
181B LYS* 3.7 10.7 + - - +
182B LYS 3.5 0.4 - - - -
183B VAL* 1.3 80.5 - - + +
185B LYS* 1.3 61.8 + - - +
186B LYS* 3.3 5.7 + - - +
54C ILE* 4.2 21.9 - - + +
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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