Contacts of the helix formed by residues 113 - 120 (chain B) in PDB entry 4X2Q
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 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B GLY 3.4 5.1 - - - +
112B LYS* 1.4 90.1 - - + +
114B PHE* 1.3 65.9 + - - +
115B LEU* 3.4 2.7 - - + +
116B GLN* 3.4 38.4 + - + +
117B ALA* 3.2 16.5 + - - +
298B GLN* 3.3 18.8 - - - +
334B PRO* 3.5 18.4 - - + +
336B ASP 5.8 0.2 - - - +
339B THR* 3.9 22.4 - - - +
340B GLU 3.6 9.2 - - - +
342B GLY 3.7 7.0 - - - +
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Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PRO* 4.4 4.3 - - + -
10B SER* 3.5 17.7 - - - -
11B PRO* 3.5 44.2 - - + -
100B ALA* 3.5 10.8 - - - -
103B ALA* 3.7 7.0 - - + -
104B THR* 3.2 44.4 - - - -
107B SER* 3.6 13.6 + - - +
112B LYS 3.5 1.0 + - - -
113B PRO* 1.3 70.7 - - - +
115B LEU* 1.3 71.3 + - + +
117B ALA* 3.2 4.4 + - - +
118B PHE* 2.9 49.9 + + + +
334B PRO 2.8 19.2 + - - +
335B PHE* 4.5 10.8 - + + +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PRO* 3.9 39.0 - - + +
113B PRO* 3.4 2.3 + - + +
114B PHE* 1.3 88.3 - - + +
116B GLN* 1.3 59.5 + - + +
118B PHE* 3.3 2.3 + - - +
119B TYR* 2.8 48.1 + - + +
337B PRO* 3.7 38.4 - - + +
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Residues in contact with GLN 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LYS* 4.2 16.2 - - - -
113B PRO* 3.4 27.8 + - + +
114B PHE 3.3 0.4 - - - -
115B LEU* 1.3 77.6 - - + +
117B ALA* 1.3 57.7 + - - +
119B TYR* 5.3 0.4 - - - -
120B VAL* 2.9 44.5 + - + +
121B ASP* 3.2 2.6 + - - +
292B GLN* 6.1 1.0 - - - +
296B PHE* 4.1 23.9 - - + -
297B ASN* 4.4 6.4 + - - -
298B GLN* 4.9 0.3 - - - +
329B ARG* 5.1 2.5 + - - +
339B THR 4.5 1.4 + - - -
340B GLU* 2.8 36.4 + - - +
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ALA* 4.0 21.8 - - + +
106B GLU* 4.3 17.5 - - + -
112B LYS* 4.5 14.3 - - + +
113B PRO 3.2 12.8 + - - +
114B PHE* 3.2 8.0 + - - +
116B GLN* 1.3 76.0 - - - +
118B PHE* 1.3 58.7 + - - +
121B ASP* 3.4 14.4 - - + +
122B LEU* 3.1 34.3 + - - +
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Residues in contact with PHE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PRO* 3.9 35.2 - - + -
99B ARG* 3.3 82.3 + - + -
100B ALA* 3.9 8.7 - - + -
103B ALA* 3.9 10.9 - - + +
114B PHE* 2.9 29.5 + + + +
115B LEU* 3.5 7.9 - - - +
116B GLN 3.2 0.2 - - - -
117B ALA* 1.3 80.7 - - - +
119B TYR* 1.3 84.8 + + + +
120B VAL 3.6 0.2 + - - -
122B LEU* 3.8 2.0 - - - +
123B GLN 3.7 7.1 + - - -
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Residues in contact with TYR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU 4.6 3.5 + - - -
9B PRO* 3.2 41.7 - - + +
99B ARG* 4.2 8.7 - - - +
115B LEU* 2.8 39.3 + - + +
116B GLN* 5.3 0.2 - - - -
118B PHE* 1.3 89.1 - + + +
120B VAL* 1.3 65.2 + - + +
123B GLN* 3.3 30.1 + - - +
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B GLN* 2.9 28.2 + - + +
119B TYR* 1.3 84.2 - - + +
121B ASP* 1.3 69.8 + - - +
122B LEU 3.4 0.4 - - - -
123B GLN* 3.4 3.7 + - - +
124B GLY* 3.0 19.2 + - - -
173B LEU* 5.0 3.3 - - + +
296B PHE* 3.7 34.1 - - + -
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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