Contacts of the helix formed by residues 170 - 178 (chain B) in PDB entry 2G9Y
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 170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169B TYR* 1.3 80.2 - - - +
171B PRO* 1.3 69.6 - - - +
172B SER 3.3 2.6 + - - -
173B ALA* 3.4 4.7 + - - +
174B THR* 2.7 33.4 + - - -
190B SER* 3.2 10.8 - - - -
192B THR* 5.0 0.2 - - - -
210B THR* 3.8 5.6 - - - -
213B GLU* 3.5 14.8 + - - -
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Residues in contact with PRO 171 (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 GLY* 1.3 82.2 - - - +
172B SER* 1.3 62.5 + - - +
174B THR* 3.6 4.4 - - - -
175B SER* 2.9 30.9 + - - +
184B GLU* 6.0 0.2 - - - +
190B SER* 3.7 2.0 - - - +
193B GLU* 3.2 29.4 - - - +
213B GLU* 3.1 22.4 - - + +
214B THR 4.0 17.3 - - - +
215B ALA* 4.4 3.1 - - - -
216B THR* 3.8 26.2 - - + +
225B LEU* 4.2 15.0 - - + -
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Residues in contact with SER 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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171B PRO* 1.3 75.4 - - - +
173B ALA* 1.3 65.2 + - - +
175B SER* 3.4 10.2 + - - -
176B GLU* 3.4 13.8 + - - +
213B GLU* 2.8 24.4 + - - -
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Residues in contact with ALA 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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167B LYS 3.3 25.4 - - - +
168B CYS* 4.0 6.5 - - - -
169B TYR* 4.0 7.0 - - + +
170B GLY 3.4 8.3 + - - +
172B SER* 1.3 79.4 + - - +
174B THR* 1.3 52.3 + - - +
176B GLU* 3.3 7.3 + - - -
177B LYS* 2.7 48.3 + - + +
213B GLU* 5.2 1.0 + - - +
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Residues in contact with THR 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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168B CYS* 3.5 17.4 + - + +
170B GLY 2.7 25.1 + - - -
171B PRO* 3.6 4.5 - - - -
173B ALA* 1.3 73.0 - - - +
175B SER* 1.3 63.3 + - - +
178B CYS* 2.7 44.4 + - + +
181B ASN* 3.8 5.4 - - + -
182B ALA* 3.4 32.8 - - - +
190B SER* 2.8 33.3 - - - +
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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
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171B PRO 2.9 24.1 + - - -
172B SER* 3.8 4.9 - - - -
174B THR* 1.3 74.1 - - - +
176B GLU* 1.3 60.4 + - - +
179B PRO* 4.0 6.4 - - - +
182B ALA* 3.8 11.9 - - - +
184B GLU* 2.7 31.2 + - - -
185B LYS* 3.9 18.4 + - - +
216B THR* 4.5 5.0 - - - +
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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 SER* 3.4 9.3 + - - +
173B ALA* 3.3 9.0 + - - +
174B THR 3.1 0.4 - - - -
175B SER* 1.3 82.3 - - - +
177B LYS* 1.3 86.7 + - + +
178B CYS 3.7 0.2 - - - -
179B PRO* 3.9 6.9 - - - +
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Residues in contact with LYS 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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164B THR* 4.0 5.0 + - - -
165B SER* 4.5 9.8 - - - +
167B LYS* 3.7 43.3 - - + +
168B CYS* 3.6 10.1 - - - -
173B ALA* 2.7 26.8 + - + +
176B GLU* 1.3 98.2 + - + +
178B CYS* 1.3 61.9 + - - +
179B PRO* 3.3 10.7 - - - +
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Residues in contact with CYS 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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163B VAL* 4.2 1.3 - - + -
164B THR* 3.5 14.1 - - - +
165B SER* 3.4 28.7 - - - -
168B CYS* 2.0 48.6 - - + -
174B THR* 2.7 16.9 + - + +
177B LYS* 1.3 75.9 - - - +
179B PRO* 1.3 55.1 - - - +
180B GLY 3.2 2.7 - - - -
181B ASN* 2.7 44.8 + - + +
182B ALA 2.9 9.7 + - - -
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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