Contacts of the helix formed by residues 165 - 171 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164J PHE* 1.4 82.6 - - + +
166J ASN* 1.3 58.5 + - - +
167J LEU 3.5 3.2 + - - -
168J LEU* 3.8 6.0 + - + -
169J ALA* 3.2 25.6 + - - +
188J LEU* 4.0 11.2 - - + -
191J LEU* 3.7 29.6 - - + +
192J ILE* 4.2 13.2 - - + -
195J VAL* 4.7 9.0 - - + -
352J LEU* 5.3 5.4 - - + -
355J TYR* 3.2 42.6 - - + +
473J LEU* 4.6 1.8 - - + -
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Residues in contact with ASN 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39J ARG 5.2 1.8 + - - -
40J ASP* 3.0 28.8 + - - +
41J GLY 4.1 5.3 + - - -
42J LEU* 3.5 21.2 - - - +
99J TYR* 5.6 0.8 - - - -
103J LEU* 4.0 6.7 - - - +
135J LEU* 3.9 21.9 - - + +
164J PHE* 3.0 24.9 + - + +
165J PRO* 1.3 69.9 - - - +
167J LEU* 1.4 67.0 + - - +
169J ALA* 4.0 0.9 - - - -
170J ASN* 2.8 56.1 + - - +
171J GLY 3.8 0.9 + - - +
355J TYR* 5.0 0.8 - - - -
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Residues in contact with LEU 167 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36J PRO* 3.7 31.0 - - + -
37J ASP 4.3 1.3 - - - +
38J VAL* 4.0 39.9 - - + +
39J ARG 5.5 0.6 + - - +
40J ASP 4.4 0.2 - - - -
41J GLY* 3.5 27.7 - - - +
165J PRO 3.5 0.6 - - - -
166J ASN* 1.4 76.0 - - - +
168J LEU* 1.3 64.8 + - + +
171J GLY* 2.9 31.5 + - - +
172J ALA* 4.3 5.8 - - + -
183J ILE* 3.9 23.9 - - + +
337J ALA* 4.2 8.5 - - + -
346J ILE* 4.5 7.9 - - + -
351J ALA* 4.8 9.2 - - + +
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Residues in contact with LEU 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165J PRO* 3.8 6.3 + - + +
166J ASN 3.3 0.2 - - - -
167J LEU* 1.3 84.1 - - + +
169J ALA* 1.3 61.4 + - - +
183J ILE* 4.1 15.7 - - + -
184J PRO 3.4 2.2 - - - +
185J PRO* 3.4 4.7 - - - +
186J HIS* 2.8 49.1 + - + +
191J LEU* 3.8 22.9 - - + -
335J MET* 4.5 13.2 - - + -
348J LEU* 3.9 22.2 - - + -
351J ALA* 4.1 23.8 - - + -
352J LEU* 3.8 29.8 - - + +
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Residues in contact with ALA 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100J ARG* 3.6 6.1 - - - +
101J TYR* 4.1 18.8 - - + -
164J PHE* 4.2 13.7 - - + -
165J PRO 3.2 21.3 + - - +
166J ASN* 3.3 8.7 + - - +
168J LEU* 1.3 76.7 - - - +
170J ASN* 1.3 59.2 + - - +
185J PRO* 3.3 6.6 - - - +
186J HIS 3.0 28.2 + - - +
188J LEU* 4.5 3.8 - - + -
191J LEU* 3.4 15.2 - - + +
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Residues in contact with ASN 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98J SER 4.8 8.1 - - - +
99J TYR* 3.3 29.0 - - + -
100J ARG* 3.1 10.3 + - - -
101J TYR* 2.8 51.5 + - - +
103J LEU* 3.7 9.7 - - - +
164J PHE* 4.6 2.6 - - - -
166J ASN* 2.8 36.6 + - - +
169J ALA* 1.3 76.7 - - - +
171J GLY* 1.3 65.3 + - - +
185J PRO* 3.5 17.2 - - - +
266J PHE* 5.5 1.6 - - - -
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Residues in contact with GLY 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41J GLY 4.7 6.1 - - - +
92J ARG* 5.7 2.5 + - - -
99J TYR* 5.7 2.1 + - - -
166J ASN* 4.6 1.7 + - - +
167J LEU 2.9 23.6 + - - +
168J LEU 3.7 0.6 + - - -
169J ALA 3.5 1.8 - - - -
170J ASN* 1.3 85.1 - - - +
172J ALA* 1.3 63.8 + - - +
183J ILE* 3.2 16.6 - - - -
184J PRO 3.9 11.9 - - - -
185J PRO* 4.7 0.4 - - - -
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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