Contacts of the helix formed by residues 165 - 179 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163T GLU* 3.7 8.9 + - + +
164T SER* 1.3 81.3 - - - +
166T PRO* 1.3 64.8 - - - +
167T GLN* 3.2 10.2 + - + +
168T PRO* 3.5 14.4 - - - +
169T GLN* 3.8 6.6 + - - +
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Residues in contact with PRO 166 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165T CYS* 1.3 72.8 - - - +
167T GLN* 1.3 59.8 + - - +
168T PRO 3.3 0.4 - - - -
169T GLN* 3.3 12.6 + - + +
170T THR* 2.9 29.5 + - - -
383T GLY 3.8 6.1 - - - +
384T VAL* 6.1 0.4 - - - -
385T ARG 4.1 22.2 - - - +
386T THR* 5.6 2.7 - - - -
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Residues in contact with GLN 167 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48T GLY 4.1 3.0 - - - +
49T HIS* 3.8 22.7 - - + -
165T CYS* 3.2 7.6 - - + +
166T PRO* 1.3 77.4 - - - +
168T PRO* 1.3 57.8 - - - +
170T THR* 3.4 6.5 + - - -
171T SER* 2.9 28.1 + - - -
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Residues in contact with PRO 168 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49T HIS* 4.0 13.3 - - + -
159T ILE* 5.4 11.9 - - + -
160T ALA 5.9 1.6 - - - +
163T GLU 5.9 0.9 - - - +
164T SER* 5.4 4.0 - - - -
165T CYS* 3.5 13.9 - - - +
166T PRO 3.3 0.4 - - - -
167T GLN* 1.3 77.2 - - - +
169T GLN* 1.3 58.9 + - - +
171T SER* 3.4 7.9 + - - -
172T GLU* 2.9 28.6 + - - +
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Residues in contact with GLN 169 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A TYR* 3.3 37.3 - - + +
584A ALA* 5.0 1.3 - - - -
165T CYS 3.8 3.2 + - - +
166T PRO* 3.3 18.2 + - + +
167T GLN 3.3 0.8 - - - -
168T PRO* 1.3 77.0 - - - +
170T THR* 1.3 60.1 + - - +
172T GLU* 3.3 6.5 + - - +
173T HIS* 2.9 27.9 + - - +
383T GLY* 4.1 6.3 - - - +
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Residues in contact with THR 170 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138T HIS* 6.0 1.1 - - - -
166T PRO 2.9 14.9 + - - -
167T GLN* 3.8 6.7 - - - -
169T GLN* 1.3 73.6 - - - +
171T SER* 1.3 58.1 + - - +
173T HIS* 3.4 1.7 + - - +
174T LEU* 2.9 29.3 + - - +
382T LEU 4.1 8.4 - - - +
383T GLY 3.4 26.3 + - - -
384T VAL* 4.6 6.5 - - - -
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Residues in contact with SER 171 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47T ILE* 4.2 9.5 - - - +
48T GLY* 3.3 41.7 - - - -
138T HIS* 5.4 5.4 - - - -
157T LEU* 6.2 2.0 - - - -
167T GLN 2.9 12.9 + - - -
168T PRO* 3.6 8.1 - - - -
169T GLN 3.3 0.2 - - - -
170T THR* 1.3 77.3 - - - +
172T GLU* 1.3 57.1 + - - +
174T LEU* 3.4 5.9 + - - +
175T ALA* 2.9 29.7 + - - +
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Residues in contact with GLU 172 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583A TYR* 5.5 4.9 - - + -
168T PRO 2.9 17.6 + - - +
169T GLN* 3.3 7.6 + - - +
171T SER* 1.3 73.2 - - - +
173T HIS* 1.3 61.3 + - - +
175T ALA* 3.4 6.3 + - - +
176T ALA* 2.9 29.5 + - - +
213T GLY* 6.4 2.2 - - - -
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Residues in contact with HIS 173 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580A SER* 4.9 7.4 - - - -
583A TYR* 4.9 9.1 - - + +
169T GLN 2.9 17.1 + - - +
170T THR 3.7 1.1 - - - +
172T GLU* 1.3 77.3 - - - +
174T LEU* 1.3 57.6 + - - +
176T ALA* 3.3 6.3 + - - +
177T ILE* 2.9 29.8 + - - +
382T LEU* 3.6 38.1 - - + +
383T GLY* 3.8 5.2 - - - +
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Residues in contact with LEU 174 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47T ILE* 5.4 4.9 - - + -
138T HIS* 4.4 17.3 - - + +
142T MET* 4.1 23.8 - - + +
170T THR 2.9 17.8 + - - +
171T SER* 3.7 7.2 - - - +
172T GLU 3.3 0.2 - - - -
173T HIS* 1.3 76.3 - - - +
175T ALA* 1.3 57.2 + - - +
177T ILE* 3.4 5.9 + - - +
178T GLU* 2.9 30.9 + - - +
382T LEU* 5.1 4.4 + - + +
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Residues in contact with ALA 175 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47T ILE* 5.7 6.9 - - + +
155T ALA* 5.2 14.1 - - + -
157T LEU* 5.9 7.2 - - + -
171T SER 2.9 17.0 + - - +
172T GLU* 3.8 7.4 - - - +
174T LEU* 1.3 75.8 - - - +
176T ALA* 1.3 62.8 + - - +
178T GLU* 4.0 5.7 - - - +
179T ILE* 3.3 25.6 + - - +
185T ILE* 5.9 6.7 - - + -
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Residues in contact with ALA 176 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579A ASN* 5.8 8.5 - - + -
172T GLU 2.9 17.9 + - - +
173T HIS* 3.7 6.5 - - - +
174T LEU 3.3 0.2 - - - -
175T ALA* 1.3 78.3 - - - +
177T ILE* 1.3 57.9 + - - +
179T ILE* 3.0 20.1 - - - +
216T ALA* 5.0 16.8 - - + -
217T GLU* 6.2 4.9 - - + -
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Residues in contact with ILE 177 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A LEU* 6.3 3.1 - - + -
142T MET* 5.6 6.1 - - + -
146T LEU* 3.8 16.8 - - + +
173T HIS 2.9 18.0 + - - +
174T LEU* 3.9 6.1 - - - +
176T ALA* 1.3 74.1 - - - +
178T GLU* 1.3 64.5 + - - +
179T ILE 4.0 2.7 - - - +
382T LEU* 5.6 7.0 - - + -
456T TRP* 4.5 24.1 - - + -
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Residues in contact with GLU 178 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142T MET* 5.1 6.3 - - - +
145T MET* 3.7 36.3 - - + +
146T LEU* 4.7 6.2 - - - -
152T MET* 5.6 4.5 - - + +
174T LEU 2.9 18.7 + - - +
175T ALA* 4.0 7.0 - - - +
176T ALA 3.3 0.4 - - - -
177T ILE* 1.3 79.7 - - - +
179T ILE* 1.3 62.9 + - + +
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Residues in contact with ILE 179 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155T ALA* 6.3 2.9 - - + -
175T ALA 3.3 13.3 + - - +
176T ALA* 3.0 19.1 - - - +
177T ILE 4.0 2.3 - - - +
178T GLU* 1.3 82.2 - - + +
184T HIS 5.2 11.9 - - - +
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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