Contacts of the helix formed by residues 174 - 184 (chain S) in PDB entry 5A0Q
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 SER 174 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36S THR* 4.2 5.4 + - - -
169S ALA* 2.0 42.5 + - - +
170S ILE* 3.6 8.1 - - - -
171S GLY 3.2 28.3 - - - -
172S SER 3.1 0.8 - - - -
173S ALA* 1.3 73.4 - - - +
175S GLU* 1.3 54.6 + - - +
177S ALA* 3.4 10.6 - - - -
178S GLN* 2.7 34.6 + - - +
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Residues in contact with GLU 175 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32S LYS* 4.5 18.7 - - - +
171S GLY 5.5 2.9 - - - +
172S SER 4.6 7.8 + - - +
173S ALA 3.3 1.6 - - - -
174S SER* 1.3 76.5 - - - +
176S GLY* 1.4 56.1 + - - +
178S GLN* 3.2 10.1 + - - +
179S SER* 3.1 26.2 + - - -
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Residues in contact with GLY 176 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173S ALA 3.2 9.1 + - - -
175S GLU* 1.4 75.5 - - - +
177S ALA* 1.4 58.3 + - - +
179S SER* 3.2 10.0 + - - -
180S SER* 3.0 28.8 + - - -
204S GLN* 4.9 1.4 - - - +
205S VAL* 5.0 2.5 - - - -
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Residues in contact with ALA 177 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36S THR* 4.9 3.1 - - - +
38S ILE* 5.0 2.2 - - + -
169S ALA* 3.7 19.7 - - + -
173S ALA 3.2 5.3 + - - -
174S SER* 3.0 15.1 + - - +
176S GLY* 1.4 72.6 - - - +
178S GLN* 1.4 60.1 + - - +
180S SER* 3.0 17.9 + - - -
181S LEU* 3.1 23.9 - - + +
201S ILE* 4.0 8.9 - - + +
205S VAL* 3.7 24.8 - - + +
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Residues in contact with GLN 178 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167S ALA 3.8 16.4 + - - -
168S ARG* 2.2 60.4 + - - +
169S ALA* 4.0 9.7 - - - +
174S SER 2.7 13.7 + - - +
175S GLU* 3.2 14.9 + - - +
177S ALA* 1.4 70.6 - - - +
179S SER* 1.4 62.2 + - - +
181S LEU* 3.2 12.6 + - - +
182S GLN* 3.1 26.7 + - - +
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Residues in contact with SER 179 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175S GLU 3.1 9.7 + - - -
176S GLY* 3.2 14.4 + - - -
178S GLN* 1.4 76.4 - - - +
180S SER* 1.4 53.2 + - - +
182S GLN* 3.0 22.6 - - - +
183S GLU* 2.7 26.3 - - - +
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Residues in contact with SER 180 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176S GLY 3.0 16.7 + - - -
177S ALA* 3.0 22.7 + - - -
179S SER* 1.4 71.2 + - - +
181S LEU* 1.3 61.2 + - - +
182S GLN 3.1 0.2 - - - -
183S GLU* 2.8 22.0 + - - +
184S VAL* 3.5 14.7 + - - +
201S ILE* 3.7 12.1 - - - +
204S GLN* 3.6 26.9 + - - -
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Residues in contact with LEU 181 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38S ILE* 4.2 9.0 - - + -
40S ILE* 4.0 18.6 - - + -
167S ALA* 3.9 33.7 - - + +
168S ARG* 4.4 0.9 - - - -
169S ALA* 3.9 29.4 - - + +
177S ALA* 3.1 19.2 + - + +
178S GLN* 3.2 14.9 + - - +
180S SER* 1.3 79.5 + - - +
182S GLN* 1.3 56.3 + - - +
184S VAL* 3.6 10.7 - - + +
185S TYR* 2.9 37.7 + - + +
189S MET* 6.3 2.0 - - + -
197S SER* 4.4 1.8 - - - +
201S ILE* 3.8 21.5 - - + -
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Residues in contact with GLN 182 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178S GLN* 3.1 15.1 + - - +
179S SER* 3.0 22.2 - - - +
180S SER 3.1 0.8 - - - -
181S LEU* 1.3 76.1 - - - +
183S GLU* 1.4 60.8 + - + +
185S TYR* 4.5 7.7 + - - +
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Residues in contact with GLU 183 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179S SER* 2.7 27.4 - - - +
180S SER* 2.8 18.7 - - - +
181S LEU 3.2 0.2 - - - -
182S GLN* 1.4 80.3 - - + +
184S VAL* 1.3 61.8 + - + +
185S TYR 3.4 5.4 + - - +
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Residues in contact with VAL 184 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180S SER 3.5 17.9 - - - +
181S LEU* 3.6 17.0 - - + +
183S GLU* 1.3 77.3 - - + +
185S TYR* 1.3 70.7 + - - +
186S HIS* 3.2 7.7 + - - +
189S MET* 3.7 10.0 - - + +
197S SER* 4.1 23.1 - - - +
201S ILE* 4.4 5.8 - - + -
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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