Contacts of the helix formed by residues 165 - 171 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164R PHE* 1.4 82.7 - - + +
166R ASN* 1.3 58.1 + - - +
167R LEU* 3.5 3.1 + - - -
168R LEU* 3.8 6.2 + - + -
169R ALA* 3.2 26.1 + - - +
188R LEU* 4.0 11.4 - - + -
191R LEU* 3.7 29.0 - - + +
192R ILE* 4.2 13.7 - - + -
195R VAL* 4.8 8.7 - - + -
352R LEU* 5.4 5.2 - - + -
355R TYR* 3.2 43.0 - - + +
473R LEU* 4.5 1.8 - - + -
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Residues in contact with ASN 166 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39R ARG 5.1 1.8 + - - -
40R ASP* 3.0 29.1 + - - +
41R GLY 4.1 5.3 + - - -
42R LEU* 3.5 21.6 - - - +
99R TYR* 5.7 0.8 - - - -
103R LEU* 4.0 7.3 - - - +
135R LEU* 3.9 21.3 - - + +
164R PHE* 3.0 25.7 + - + +
165R PRO* 1.3 70.3 - - - +
167R LEU* 1.3 65.7 + - - +
169R ALA* 4.0 0.9 - - - -
170R ASN* 2.8 54.9 + - - +
171R GLY 3.8 1.5 + - - +
355R TYR* 4.9 0.8 - - - -
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Residues in contact with LEU 167 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36R PRO* 3.7 31.6 - - + -
37R ASP 4.2 1.8 - - - +
38R VAL* 4.0 39.9 - - + +
39R ARG 5.5 0.8 + - - +
41R GLY* 3.5 28.8 - - - +
165R PRO 3.5 0.6 - - - -
166R ASN* 1.3 76.8 - - - +
168R LEU* 1.3 62.3 + - + +
171R GLY* 2.9 31.3 + - - +
172R ALA* 4.5 4.0 - - + -
183R ILE* 3.9 23.5 - - + +
337R ALA* 4.2 9.2 - - + -
346R ILE* 4.5 7.2 - - + -
351R ALA* 4.8 9.0 - - + +
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Residues in contact with LEU 168 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165R PRO* 3.8 6.3 + - + +
166R ASN 3.3 0.2 - - - -
167R LEU* 1.3 84.5 - - + +
169R ALA* 1.3 61.3 - - - +
183R ILE* 4.1 16.4 - - + -
184R PRO 3.4 5.5 - - - +
185R PRO* 3.4 0.3 - - - +
186R HIS* 2.8 49.4 + - + +
191R LEU* 3.7 22.4 - - + -
234R TYR* 6.0 0.2 - - + -
335R MET* 4.5 13.9 - - - -
348R LEU* 3.9 20.9 - - + -
351R ALA* 4.1 23.3 - - + -
352R LEU* 3.8 28.9 - - + +
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Residues in contact with ALA 169 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100R ARG* 3.6 6.2 - - - +
101R TYR* 4.1 19.5 - - + -
164R PHE* 4.2 13.5 - - + -
165R PRO 3.2 21.1 + - - +
166R ASN* 3.4 8.7 + - - +
168R LEU* 1.3 76.4 - - - +
170R ASN* 1.3 59.1 + - - +
185R PRO* 3.3 6.6 - - - +
186R HIS 3.0 28.2 + - - +
188R LEU* 4.6 4.3 - - + -
191R LEU* 3.4 15.7 - - + +
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Residues in contact with ASN 170 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98R SER 4.9 7.6 - - - +
99R TYR* 3.3 28.4 - - + -
100R ARG 3.1 9.5 + - - -
101R TYR* 2.8 52.9 + - - +
103R LEU* 3.7 9.5 - - - +
164R PHE* 4.6 2.0 - - - -
166R ASN* 2.8 36.4 + - - +
169R ALA* 1.3 77.3 - - - +
171R GLY* 1.3 64.1 + - - +
185R PRO* 3.5 17.7 - - - +
266R PHE* 5.5 1.6 - - - -
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Residues in contact with GLY 171 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41R GLY 4.7 6.6 - - - +
92R ARG* 5.7 1.9 + - - -
99R TYR* 5.6 3.1 + - - -
166R ASN* 4.5 1.4 + - - +
167R LEU 2.9 23.4 + - - +
168R LEU 3.7 1.0 + - - -
169R ALA 3.5 1.8 - - - -
170R ASN* 1.3 86.5 - - - +
172R ALA* 1.3 65.3 + - - +
183R ILE* 3.2 17.3 - - - -
184R PRO 3.9 11.2 - - - -
185R 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