Contacts of the helix formed by residues 91 - 98 (chain G) in PDB entry 4JCQ
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 SER 91 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60G GLN 3.9 12.2 + - - -
61G GLY* 4.3 2.0 - - - -
62G GLY 5.2 1.3 - - - -
90G ALA* 1.3 73.7 - - - +
92G ALA* 1.3 61.9 + - - -
94G ILE* 3.0 16.9 + - - +
95G THR* 3.3 5.9 + - - -
114G MET* 3.0 18.2 + - - +
116G HIS* 2.7 32.9 + - - -
117G GLN* 3.1 23.7 + - - +
118G PRO* 4.1 18.1 - - - +
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Residues in contact with ALA 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G ILE* 4.3 9.6 - - + -
61G GLY* 3.9 1.9 - - - -
62G GLY 3.8 24.9 - - - +
63G HIS 4.3 17.5 - - - +
64G VAL* 4.9 4.9 - - - -
67G GLY* 4.6 6.5 - - - -
90G ALA 3.2 0.2 + - - -
91G SER* 1.3 80.0 - - - +
93G GLY* 1.3 61.1 + - - +
95G THR* 3.3 12.2 + - - -
96G ILE* 3.2 28.7 + - - +
117G GLN* 3.8 4.1 + - - +
118G PRO* 5.4 0.8 - - + +
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Residues in contact with GLY 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G ILE* 4.3 0.6 - - - +
57G ILE* 4.4 5.7 - - - +
59G SER* 4.5 18.8 - - - -
61G GLY* 3.8 3.4 - - - -
89G VAL* 3.5 12.9 - - - +
90G ALA 2.8 13.1 + - - -
92G ALA* 1.3 78.8 - - - +
94G ILE* 1.3 55.6 + - - +
96G ILE* 3.5 11.7 + - - +
97G TYR* 3.0 27.9 + - - +
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Residues in contact with ILE 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G VAL* 3.5 23.8 - - + +
90G ALA* 3.6 2.9 + - - -
91G SER 3.0 11.5 + - - +
93G GLY* 1.3 74.1 - - - +
95G THR* 1.3 60.4 + - - +
97G TYR* 3.2 2.4 + - + +
98G LEU* 2.9 50.1 + - + +
113G TYR* 3.8 25.4 - - + -
114G MET 3.3 25.1 - - - +
115G ILE* 4.0 23.1 - - + -
117G GLN* 4.4 0.9 - - - +
147G ILE* 4.4 12.3 - - + -
178G ILE* 4.1 15.5 - - + -
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Residues in contact with THR 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G GLY* 4.7 5.8 - - - +
68G ASP* 4.4 13.9 - - - +
71G HIS* 3.1 35.0 - - + -
91G SER 3.3 10.2 + - - -
92G ALA* 3.3 13.1 + - - -
94G ILE* 1.3 81.4 - - - +
96G ILE* 1.3 61.5 + - - +
98G LEU* 3.4 8.2 + - - +
99G ALA 3.5 0.3 + - - -
117G GLN* 4.0 14.2 + - - -
143G ILE* 4.2 14.5 - - + +
146G LEU* 4.0 33.4 - - + +
147G ILE* 4.9 1.7 - - - +
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Residues in contact with ILE 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G ILE* 4.1 10.1 - - + -
30G ILE* 3.6 37.7 - - + -
57G ILE* 4.0 17.4 - - + +
67G GLY* 3.7 19.3 - - - +
70G ILE* 3.7 41.1 - - + -
71G HIS* 4.3 6.7 - - - +
74G ILE* 3.8 13.1 - - + +
83G VAL* 4.8 1.4 - - - +
92G ALA 3.2 15.0 + - - +
93G GLY* 3.7 7.4 - - - +
95G THR* 1.3 74.5 - - - +
97G TYR* 1.3 65.7 + - - +
99G ALA* 3.0 20.8 + - - +
100G ALA 4.4 0.5 + - - -
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Residues in contact with TYR 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G ILE* 3.8 19.7 - - + -
83G VAL* 3.4 25.8 - - + +
85G GLY* 3.6 21.8 - - - -
89G VAL* 3.9 16.6 - - + -
93G GLY 3.0 19.4 + - - +
94G ILE* 3.5 5.4 - - + +
96G ILE* 1.3 76.2 - - - +
98G LEU* 1.3 60.9 + - + +
99G ALA 3.2 3.6 + - - -
100G ALA* 3.6 3.8 + - - +
105G ARG* 3.4 31.5 - - + +
106G PHE 2.7 38.9 + - - -
113G TYR* 4.1 8.5 - + - -
178G ILE* 3.3 42.6 - - + -
179G VAL* 3.6 12.6 - - - +
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Residues in contact with LEU 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G HIS* 4.5 4.8 + - - -
75G LYS* 4.9 3.6 + - - -
94G ILE* 2.9 38.4 + - + +
95G THR 3.4 6.0 + - - +
96G ILE 3.2 0.6 - - - -
97G TYR* 1.3 74.3 - - + +
99G ALA* 1.3 62.4 + - - +
100G ALA 3.3 9.0 - - - +
105G ARG* 3.6 35.4 + - - +
146G LEU* 4.7 5.7 - - + +
147G ILE* 3.8 37.9 - - + -
150G ALA* 3.8 20.3 - - + +
151G THR* 4.0 16.8 - - + -
178G ILE* 4.2 17.3 - - + -
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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