Contacts of the helix formed by residues 106 - 113 (chain C) in PDB entry 4GKH
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 ALA 106 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105C THR* 1.3 72.8 - - - +
107C PHE* 1.3 63.1 + - - +
109C VAL* 3.2 12.7 - - - +
110C LEU* 2.9 27.5 + - - +
120C ILE* 4.5 4.8 - - + +
124C LEU* 4.3 10.3 - - + -
201C LEU* 3.2 30.7 + - + +
204C LEU* 2.9 14.3 + - + +
206C PHE* 3.6 23.1 - - + -
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Residues in contact with PHE 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B THR* 4.9 4.3 - - + -
105C THR* 3.1 7.4 - - - +
106C ALA* 1.3 77.5 - - - +
108C GLN* 1.3 69.4 + - + +
110C LEU* 3.4 5.3 + - - +
111C GLU* 3.1 61.0 + - - +
201C LEU* 3.0 31.0 + - + +
202C ASP* 3.8 7.6 - - - +
238C GLU* 4.0 11.9 - - - -
239C PHE* 3.7 29.8 - + - -
3D HIS* 3.7 59.7 - + + -
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Residues in contact with GLN 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C GLY 4.8 0.5 - - - +
104C LYS* 3.4 27.0 - - + +
105C THR* 2.9 46.2 + - - +
107C PHE* 1.3 83.8 - - + +
109C VAL* 1.3 57.1 + - - +
111C GLU* 3.3 8.2 + - - +
112C GLU* 2.9 30.9 + - - +
3D HIS 6.0 0.7 - - - +
5D GLN* 3.0 35.4 + - - +
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Residues in contact with VAL 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C LYS* 3.7 27.6 - - + -
105C THR 3.0 17.2 + - - +
106C ALA* 3.2 21.8 - - - +
108C GLN* 1.3 76.7 - - - +
110C LEU* 1.3 53.0 + - - +
112C GLU* 4.3 6.3 - - - -
113C TYR* 2.7 51.4 + - + +
120C ILE* 3.9 18.5 - - + +
206C PHE* 3.9 31.2 - - + +
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Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ARG* 4.4 14.5 + - - +
106C ALA 2.9 18.0 + - - +
107C PHE 3.7 4.3 - - - +
109C VAL* 1.3 78.4 - - - +
111C GLU* 1.3 61.7 + - - +
113C TYR 4.4 1.3 - - - +
114C PRO* 3.3 26.2 - - - +
117C GLY* 3.5 34.3 - - - +
120C ILE* 3.8 17.7 - - + -
121C VAL* 6.0 0.4 - - + -
201C LEU* 4.2 14.8 - - + -
236C LEU* 4.5 11.9 - - + -
239C PHE* 3.8 44.3 - - + -
243C LEU* 4.6 6.1 - - + -
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Residues in contact with GLU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B THR* 3.5 14.6 - - - -
9B SER* 2.9 39.7 + - - +
10B CYS* 3.3 10.8 - - - +
11B SER 2.9 23.6 + - - -
107C PHE* 3.1 50.7 + - + +
108C GLN* 3.7 7.6 - - - +
110C LEU* 1.3 76.5 - - - +
112C GLU* 1.3 59.7 + - - +
114C PRO* 3.5 4.5 - - - +
239C PHE* 4.3 12.6 - - + -
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Residues in contact with GLU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B SER* 3.5 27.6 - - - +
12B ARG 4.7 2.9 - - - +
104C LYS* 2.7 40.3 + - - +
108C GLN* 2.9 16.8 + - - +
109C VAL* 3.9 3.4 - - - +
110C LEU 3.3 0.2 - - - -
111C GLU* 1.3 79.6 - - - +
113C TYR* 1.3 98.9 + - + +
114C PRO* 3.4 6.2 - - - +
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Residues in contact with TYR 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 3.6 34.8 - - - +
104C LYS* 5.0 1.0 + - + -
109C VAL* 2.7 36.5 + - + +
110C LEU* 3.4 8.0 - - - +
112C GLU* 1.3 116.1 + - + +
114C PRO* 1.3 60.5 - - - +
115C ASP* 3.1 3.6 - - + -
116C SER* 2.8 40.6 + - - +
117C GLY 3.9 1.9 + - - -
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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