Contacts of the helix formed by residues 91 - 98 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A GLN 3.9 11.7 + - - -
61A GLY* 4.3 2.5 - - - -
62A GLY 5.2 1.8 - - - -
90A ALA* 1.3 74.8 - - - +
92A ALA* 1.3 60.2 + - - -
94A ILE* 3.0 17.9 + - - +
95A THR* 3.3 5.9 + - - -
114A MET* 3.0 17.8 + - - +
116A HIS* 2.7 35.0 + - - -
117A GLN* 3.1 22.8 + - - +
118A PRO* 4.1 18.1 - - - +
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 4.3 10.3 - - + -
61A GLY* 3.9 1.5 - - - -
62A GLY 3.8 25.1 - - - +
63A HIS 4.3 17.5 - - - +
64A VAL* 4.9 5.8 - - - -
67A GLY* 4.6 5.2 - - - -
90A ALA 3.2 0.6 + - - -
91A SER* 1.3 79.2 - - - +
93A GLY* 1.3 60.3 + - - +
95A THR* 3.4 11.8 + - - -
96A ILE* 3.2 28.4 + - - +
117A GLN* 3.8 4.4 + - - +
118A PRO* 5.4 0.8 - - - +
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Residues in contact with GLY 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 4.6 0.7 - - - -
57A ILE* 4.4 5.5 - - - +
59A SER* 4.5 18.6 - - - -
61A GLY* 3.8 4.0 - - - -
89A VAL* 3.5 12.5 - - - +
90A ALA 2.8 13.2 + - - -
92A ALA* 1.3 76.4 - - - +
94A ILE* 1.3 57.9 + - - +
96A ILE* 3.5 11.7 + - - +
97A TYR* 2.9 27.9 + - - +
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Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A VAL* 3.5 25.4 - - + +
90A ALA* 3.6 2.7 + - - -
91A SER 3.0 12.6 + - - +
93A GLY* 1.3 74.7 - - - +
95A THR* 1.3 59.3 + - - +
97A TYR* 3.2 2.7 + - + +
98A LEU* 2.9 50.0 + - + +
113A TYR* 3.8 25.4 - - + -
114A MET 3.3 24.2 - - - +
115A ILE* 4.0 23.8 - - + -
117A GLN* 4.4 0.9 - - - +
147A ILE* 4.4 12.8 - - + -
178A ILE* 4.1 15.5 - - + -
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Residues in contact with THR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A GLY* 4.7 5.4 - - - +
68A ASP* 4.4 13.9 - - - +
71A HIS* 3.1 34.4 - - + -
91A SER 3.3 10.2 + - - -
92A ALA* 3.4 12.3 + - - -
94A ILE* 1.3 81.5 - - - +
96A ILE* 1.3 61.1 + - - +
98A LEU* 3.4 8.1 + - - +
99A ALA 3.5 0.5 + - - -
117A GLN* 4.0 14.2 + - - -
143A ILE* 4.2 15.6 - - + +
146A LEU* 4.0 33.2 - - + -
147A ILE* 4.9 2.0 - - - +
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Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 4.1 10.8 - - + -
30A ILE* 3.6 37.9 - - + -
57A ILE* 4.0 18.3 - - + +
67A GLY* 3.7 18.2 - - - +
70A ILE* 3.7 42.2 - - + -
71A HIS* 4.3 7.0 - - - +
74A ILE* 3.8 12.2 - - + +
83A VAL* 4.8 1.4 - - - +
92A ALA 3.2 13.5 + - - +
93A GLY* 3.7 7.0 - - - +
94A ILE 3.3 0.2 - - - -
95A THR* 1.3 73.6 - - - +
97A TYR* 1.3 66.8 + - - +
99A ALA* 3.0 20.6 + - - +
100A ALA 4.4 0.3 + - - -
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Residues in contact with TYR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ILE* 3.8 19.3 - - + -
83A VAL* 3.4 25.5 - - + +
85A GLY* 3.6 21.5 - - - -
89A VAL* 3.9 16.8 - - + -
93A GLY 2.9 18.3 + - - +
94A ILE* 3.5 4.9 - - - +
96A ILE* 1.3 76.2 - - - +
98A LEU* 1.3 62.1 + - + +
99A ALA 3.2 4.0 + - - -
100A ALA* 3.6 4.0 + - - +
105A ARG* 3.4 32.2 - - + +
106A PHE 2.7 39.6 + - - -
113A TYR* 4.0 8.1 - + - -
178A ILE* 3.3 41.7 - - + -
179A VAL* 3.5 12.8 - - - +
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A HIS* 4.5 4.0 + - - -
75A LYS* 4.9 3.6 + - - -
94A ILE* 2.9 38.6 + - + +
95A THR 3.9 5.8 - - - +
96A ILE 3.2 0.4 - - - -
97A TYR* 1.3 75.5 - - + +
99A ALA* 1.3 63.7 + - - +
100A ALA 3.2 9.2 - - - +
105A ARG* 3.6 34.8 - - - +
146A LEU* 4.7 6.0 - - + +
147A ILE* 3.8 38.1 - - + -
150A ALA* 3.8 23.5 - - + +
151A THR* 4.0 13.7 - - + -
178A ILE* 4.2 17.5 - - + -
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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