Contacts of the helix formed by residues 165 - 179 (chain S) in PDB entry 6O81
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 CYS 165 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163S GLU* 3.7 9.8 - - + +
164S SER* 1.3 82.0 - - - +
166S PRO* 1.3 66.6 - - - +
167S GLN* 3.2 9.5 + - + +
168S PRO* 3.5 13.8 - - - +
169S GLN* 3.8 6.4 + - - +
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Residues in contact with PRO 166 (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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165S CYS* 1.3 73.1 - - - +
167S GLN* 1.3 59.1 + - - +
168S PRO 3.3 0.2 - - - -
169S GLN* 3.3 11.7 + - + +
170S THR* 2.9 29.3 + - - -
383S GLY 3.8 6.3 - - - +
384S VAL* 6.1 0.2 - - - -
385S ARG 4.1 22.4 - - - +
386S THR* 5.6 2.0 - - - -
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Residues in contact with GLN 167 (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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48S GLY 4.1 3.2 - - - +
49S HIS* 3.8 23.3 - - + -
165S CYS* 3.2 7.2 - - + +
166S PRO* 1.3 78.5 - - - +
168S PRO* 1.3 57.3 - - - +
170S THR* 3.4 7.0 + - - -
171S SER* 2.9 27.4 + - - -
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Residues in contact with PRO 168 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49S HIS* 4.0 11.7 - - + +
159S ILE* 5.4 12.6 - - + -
160S ALA 5.9 1.6 - - - +
163S GLU 6.0 1.1 - - - +
164S SER* 5.4 4.5 - - - -
165S CYS 3.5 13.5 - - - +
166S PRO 3.3 0.4 - - - -
167S GLN* 1.3 76.8 - - - +
169S GLN* 1.3 59.8 + - - +
171S SER* 3.4 8.2 + - - -
172S GLU* 2.9 28.9 + - - +
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Residues in contact with GLN 169 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B TYR* 3.7 30.4 - - + +
584B ALA* 5.5 0.7 - - - -
586B ASN* 6.4 0.2 - - + -
165S CYS 3.8 2.7 + - - +
166S PRO* 3.3 18.2 + - + +
167S GLN 3.3 0.4 - - - -
168S PRO* 1.3 75.9 - - - +
170S THR* 1.3 58.8 + - - +
172S GLU* 3.3 6.9 + - - +
173S HIS* 2.9 28.2 + - - +
383S GLY* 4.1 8.5 - - - +
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Residues in contact with THR 170 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138S HIS* 5.6 1.7 - - - +
166S PRO 2.9 14.0 + - - -
167S GLN* 3.8 7.2 - - - -
169S GLN* 1.3 74.7 - - - +
171S SER* 1.3 58.6 + - - +
173S HIS* 3.4 1.9 + - - +
174S LEU* 2.9 29.1 + - - +
382S LEU 4.1 8.1 - - - +
383S GLY 3.4 25.9 + - - -
384S VAL* 4.6 6.3 - - - -
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Residues in contact with SER 171 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47S ILE* 4.2 9.7 - - - +
48S GLY* 3.3 42.2 - - - -
138S HIS* 5.4 5.2 - - - -
157S LEU* 6.2 1.8 - - - -
167S GLN 2.9 13.6 + - - -
168S PRO* 3.6 7.4 - - - -
169S GLN 3.3 0.2 - - - -
170S THR* 1.3 77.5 - - - +
172S GLU* 1.3 57.1 + - - +
174S LEU* 3.4 5.7 + - - +
175S ALA* 2.9 29.5 + - - +
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Residues in contact with GLU 172 (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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583B TYR* 5.8 3.8 - - + -
168S PRO 2.9 17.4 + - - +
169S GLN* 3.7 7.2 - - - +
171S SER* 1.3 74.3 - - - +
173S HIS* 1.3 60.8 + - - +
175S ALA* 3.4 6.9 + - - +
176S ALA* 2.9 29.3 + - - +
213S GLY* 6.4 2.7 - - - -
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Residues in contact with HIS 173 (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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580B SER* 5.2 6.5 - - - -
583B TYR* 4.7 10.2 - - + +
169S GLN 2.9 17.2 + - - +
170S THR 3.7 0.9 - - - +
172S GLU* 1.3 77.6 - - - +
174S LEU* 1.3 57.1 + - - +
176S ALA* 3.3 7.0 + - - +
177S ILE* 2.9 29.8 + - - +
382S LEU* 3.6 37.7 - - + +
383S GLY* 3.8 4.9 - - - +
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Residues in contact with LEU 174 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47S ILE* 5.4 5.4 - - + -
138S HIS* 4.4 17.5 - - + +
139S ASP* 6.0 0.2 - - - -
142S MET* 4.1 24.1 - - + +
170S THR 2.9 17.4 + - - +
171S SER* 3.7 7.2 - - - +
173S HIS* 1.3 75.1 - - - +
175S ALA* 1.3 58.0 + - - +
177S ILE* 3.4 6.1 + - - +
178S GLU* 2.9 29.9 + - - +
382S LEU* 5.1 3.7 + - + +
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Residues in contact with ALA 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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47S ILE* 5.7 6.7 - - + +
155S ALA* 5.2 15.7 - - + -
157S LEU* 5.9 6.5 - - + -
171S SER 2.9 17.4 + - - +
172S GLU* 3.8 7.4 - - - +
173S HIS 3.3 0.2 - - - -
174S LEU* 1.3 75.6 - - - +
176S ALA* 1.3 62.3 + - - +
178S GLU* 4.0 5.2 - - - +
179S ILE* 3.3 25.8 + - - +
185S ILE* 5.9 6.5 - - + -
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Residues in contact with ALA 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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579B ASN* 5.9 7.4 - - + -
172S GLU 2.9 18.1 + - - +
173S HIS* 3.7 7.0 - - - +
175S ALA* 1.3 77.7 - - - +
177S ILE* 1.3 58.4 + - - +
179S ILE* 3.0 19.9 - - - +
216S ALA* 5.0 16.6 - - + -
217S GLU* 6.2 4.5 - - + -
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Residues in contact with ILE 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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576B LEU* 6.6 0.2 - - + -
142S MET* 5.6 5.6 - - + -
146S LEU* 3.8 17.5 - - + +
173S HIS 2.9 17.4 + - - +
174S LEU* 3.9 6.5 - - - +
175S ALA 3.4 0.2 - - - -
176S ALA* 1.3 75.9 - - - +
178S GLU* 1.3 63.6 + - - +
179S ILE 4.0 1.7 - - - +
382S LEU* 5.6 7.9 - - + -
456S TRP* 4.5 24.1 - - + -
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Residues in contact with GLU 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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142S MET* 5.1 6.0 - - - +
145S MET* 3.7 37.1 - - + +
146S LEU* 4.7 5.9 - - - +
152S MET* 5.6 4.0 - - + +
174S LEU 2.9 17.1 + - - +
175S ALA* 4.0 7.2 - - - +
176S ALA 3.3 0.4 - - - -
177S ILE* 1.3 81.3 - - - +
179S ILE* 1.3 63.6 + - + +
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Residues in contact with ILE 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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155S ALA* 6.3 2.5 - - + -
175S ALA 3.3 13.7 + - - +
176S ALA* 3.0 20.1 - - - +
177S ILE 4.0 2.3 - - - +
178S GLU* 1.3 83.3 - - + +
184S HIS 5.2 12.1 - - - +
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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