Contacts of the helix formed by residues 112 - 117 (chain C) in PDB entry 4GCK
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 HIS 112 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107C ARG* 3.3 15.1 + - + +
110C THR* 2.7 34.7 + - + -
111C GLY* 1.3 76.8 - - - +
113C ALA* 1.3 62.1 + - - +
115C MET* 3.1 25.8 + - - +
116C PHE* 4.2 0.7 - - - -
171C SER* 5.1 10.3 - - - -
174C VAL* 3.8 19.2 - - + +
175C ARG* 6.5 0.2 - - + -
110D THR 2.8 26.0 + - - -
111D GLY* 3.6 26.0 - - - -
112D HIS* 3.5 21.9 - + - -
115D MET* 3.6 26.4 - - - +
122D GLN* 5.6 1.5 + - - -
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Residues in contact with ALA 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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23C LEU* 3.8 24.2 - - + -
28C GLY 5.2 0.7 - - - -
59C PHE* 4.5 7.2 - - + -
107C ARG* 2.9 36.5 + - + +
108C ILE* 3.8 19.3 - - + -
112C HIS* 1.3 74.3 - - - +
114C LEU* 1.3 61.4 + - - +
115C MET 3.4 0.9 + - - -
116C PHE* 3.5 23.4 + - - -
117C GLU* 4.1 9.2 - - - +
115D MET* 4.8 0.9 - - - -
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Residues in contact with LEU 114 (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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59C PHE* 3.9 27.8 - - + -
63C ILE* 4.6 1.8 - - + -
108C ILE* 3.8 25.6 - - + +
111C GLY 3.6 8.3 - - - +
112C HIS 3.1 1.2 - - - -
113C ALA* 1.3 75.7 - - - +
115C MET* 1.3 66.2 + - - +
116C PHE 3.1 3.4 - - - -
117C GLU* 3.0 24.2 + - + +
118C GLN 4.9 1.3 - - - +
119C ASP* 5.9 0.5 - - - -
121C LEU* 3.9 25.1 - - + -
122C GLN* 3.8 46.2 - - + +
125C ILE* 3.8 21.1 - - + -
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Residues in contact with MET 115 (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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111C GLY 3.5 13.4 + - - +
112C HIS* 3.1 20.3 + - - +
114C LEU* 1.3 82.6 - - + +
116C PHE* 1.3 59.8 + - + +
117C GLU 4.4 2.6 - - - +
119C ASP* 5.7 2.2 - - - +
122C GLN* 5.2 10.3 - - + +
28D GLY 5.7 1.1 - - - +
29D SER* 3.8 34.7 - - - +
30D GLN* 4.7 4.0 - - - +
107D ARG* 6.3 0.7 - - - -
112D HIS* 3.7 42.8 - - + +
115D MET* 3.8 13.2 - - + -
116D PHE* 3.4 31.7 - - + -
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Residues in contact with PHE 116 (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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28C GLY 4.9 1.1 - - - -
30C GLN 3.6 13.7 - - - -
31C ARG* 2.8 78.4 + - + +
32C ILE* 5.0 2.0 - - + -
112C HIS 4.2 2.9 - - - -
113C ALA* 3.5 19.1 - - - -
114C LEU 3.1 0.8 - - - -
115C MET* 1.3 75.7 - - - +
117C GLU* 1.3 76.4 + - - +
31D ARG* 5.5 3.4 - - - -
115D MET* 3.5 55.2 - - + -
116D PHE* 4.0 25.8 - + - -
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Residues in contact with GLU 117 (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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31C ARG* 5.2 0.3 + - - -
32C ILE 5.2 2.9 + - - -
55C LYS* 2.6 39.1 + - - +
56C THR* 4.7 8.8 + - - -
59C PHE* 3.7 38.6 - - + -
113C ALA 4.1 10.8 - - - +
114C LEU* 3.0 18.2 + - - +
115C MET 4.4 2.8 - - - +
116C PHE* 1.3 97.8 - - - +
118C GLN* 1.3 69.7 + - - +
119C ASP* 3.4 6.8 + - - +
121C LEU* 3.6 19.7 - - + -
8W A 6.1 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