Contacts of the helix formed by residues 165 - 171 (chain T) in PDB entry 6QX2
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 PRO 165 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164T PHE* 1.4 81.5 - - + +
166T ASN* 1.3 58.2 + - - +
167T LEU* 3.5 2.8 + - - -
168T LEU* 3.8 6.2 + - + -
169T ALA* 3.2 25.5 + - - +
188T LEU* 4.0 10.5 - - + -
191T LEU* 3.7 29.4 - - + +
192T ILE* 4.2 13.2 - - + -
195T VAL* 4.7 8.7 - - + -
352T LEU* 5.4 5.6 - - + -
355T TYR* 3.2 41.7 - - + +
473T LEU* 4.6 1.8 - - + -
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Residues in contact with ASN 166 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39T ARG 5.2 2.0 + - - -
40T ASP* 3.0 28.7 + - - +
41T GLY 4.1 5.3 + - - -
42T LEU* 3.5 21.8 - - - +
99T TYR* 5.7 0.8 - - - -
103T LEU* 4.0 8.3 - - - +
135T LEU* 3.9 20.1 - - + +
164T PHE* 3.0 25.6 + - + +
165T PRO* 1.3 70.3 - - - +
167T LEU* 1.3 66.4 + - - +
169T ALA* 3.7 1.3 - - - -
170T ASN* 2.8 54.8 + - - +
171T GLY 3.8 1.6 + - - +
355T TYR* 4.9 0.8 - - - -
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Residues in contact with LEU 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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36T PRO* 3.7 30.7 - - + -
37T ASP 4.3 1.3 - - - +
38T VAL* 4.0 39.7 - - + +
39T ARG 5.5 0.2 + - - -
41T GLY* 3.5 29.0 - - - +
165T PRO 3.5 1.0 - - - -
166T ASN* 1.3 76.2 - - - +
168T LEU* 1.3 63.1 + - + +
171T GLY* 2.9 31.6 + - - +
172T ALA* 4.5 4.5 - - + -
183T ILE* 3.9 24.6 - - + +
337T ALA* 4.2 9.2 - - + -
346T ILE* 4.4 8.1 - - + -
351T ALA* 4.8 9.0 - - + +
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Residues in contact with LEU 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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165T PRO* 3.8 6.5 + - + +
166T ASN 3.3 0.2 - - - -
167T LEU* 1.3 84.3 - - + +
169T ALA* 1.3 61.1 + - - +
183T ILE* 4.1 15.0 - - + -
184T PRO 3.4 2.6 - - - +
185T PRO* 3.4 4.5 - - - +
186T HIS* 2.8 50.4 + - + +
191T LEU* 3.7 22.0 - - + -
234T TYR* 6.0 0.2 - - + -
335T MET* 4.2 15.0 - - - -
348T LEU* 3.9 21.5 - - + -
351T ALA* 4.1 22.7 - - + -
352T LEU* 3.8 29.8 - - + +
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Residues in contact with ALA 169 (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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100T ARG* 3.6 6.6 - - - +
101T TYR* 4.1 18.8 - - + -
164T PHE* 4.2 14.4 - - + -
165T PRO 3.2 20.9 + - - +
166T ASN* 3.4 8.3 + - - +
168T LEU* 1.3 77.7 - - - +
170T ASN* 1.3 59.1 + - + +
185T PRO* 3.3 6.6 - - - +
186T HIS 3.0 28.4 + - - +
188T LEU* 4.5 4.3 - - + -
191T LEU* 3.4 15.2 - - + +
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Residues in contact with ASN 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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98T SER 4.9 8.0 - - - +
99T TYR* 3.3 28.9 - - + -
100T ARG* 3.1 9.6 + - - -
101T TYR* 2.8 51.6 + - - +
103T LEU* 3.7 9.5 - - - +
164T PHE* 4.6 2.6 - - - -
166T ASN* 2.8 35.4 + - - +
169T ALA* 1.3 77.6 - - - +
171T GLY* 1.3 64.4 + - - +
185T PRO* 3.5 16.7 - - - +
266T PHE* 5.5 1.4 - - - -
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Residues in contact with GLY 171 (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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41T GLY 4.6 6.6 - - - +
99T TYR* 5.7 2.3 + - - -
166T ASN* 4.5 1.4 + - - +
167T LEU 2.9 23.3 + - - +
168T LEU 3.7 0.6 + - - -
169T ALA 3.5 1.8 - - - -
170T ASN* 1.3 86.5 - - - +
172T ALA* 1.3 66.1 + - - +
183T ILE* 3.2 17.0 - - - -
184T PRO 3.9 11.2 - - - -
185T PRO* 4.8 0.2 - - - -
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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