Contacts of the helix formed by residues 91 - 98 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60D GLN 3.9 11.7 + - - -
61D GLY* 4.3 2.5 - - - -
62D GLY 5.2 1.1 - - - -
90D ALA* 1.3 74.3 - - - +
92D ALA* 1.3 60.2 + - - -
94D ILE* 3.0 16.9 + - - +
95D THR* 3.3 6.4 + - - -
114D MET* 3.0 18.6 + - - +
116D HIS* 2.7 32.9 + - - -
117D GLN* 3.1 24.1 + - - +
118D PRO* 4.1 18.4 - - - +
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Residues in contact with ALA 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ILE* 4.3 9.6 - - + -
61D GLY* 3.9 1.7 - - - -
62D GLY 3.8 25.4 - - - +
63D HIS 4.3 17.7 - - - +
64D VAL* 4.9 4.7 - - - -
67D GLY* 4.6 5.8 - - - -
90D ALA 3.2 0.2 + - - -
91D SER* 1.3 80.2 - - - +
93D GLY* 1.3 60.2 + - - +
95D THR* 3.3 12.0 + - - -
96D ILE* 3.2 28.2 + - - +
117D GLN* 3.8 4.2 + - - +
118D PRO* 5.4 0.6 - - - +
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Residues in contact with GLY 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ILE* 4.3 0.4 - - - +
57D ILE* 4.4 5.1 - - - +
59D SER* 4.5 19.1 - - - -
61D GLY* 3.8 4.2 - - - -
89D VAL* 3.5 12.9 - - - +
90D ALA 2.8 13.8 + - - -
92D ALA* 1.3 77.3 - - - +
94D ILE* 1.3 55.8 + - - +
96D ILE* 3.5 11.3 + - - +
97D TYR* 2.9 28.4 + - - +
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Residues in contact with ILE 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D VAL* 3.5 24.7 - - + +
90D ALA* 3.6 2.9 + - - -
91D SER 3.0 13.0 + - - +
93D GLY* 1.3 73.4 - - - +
95D THR* 1.3 59.6 + - - +
97D TYR* 3.2 3.0 + - + +
98D LEU* 2.9 49.7 + - + +
113D TYR* 3.8 24.7 - - + -
114D MET 3.3 24.7 - - - +
115D ILE* 4.0 24.2 - - + -
117D GLN* 4.4 0.4 - - - +
147D ILE* 4.4 12.1 - - + -
178D ILE* 4.1 15.7 - - + -
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Residues in contact with THR 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D GLY 4.7 5.8 - - - +
68D ASP* 4.4 13.2 - - - +
71D HIS* 3.1 35.2 - - + -
91D SER 3.3 9.8 + - - -
92D ALA* 3.3 12.5 + - - -
94D ILE* 1.3 81.4 - - - +
96D ILE* 1.3 61.3 + - - +
98D LEU* 3.5 8.2 + - - +
99D ALA 3.5 0.3 + - - -
117D GLN* 4.0 13.9 + - - -
143D ILE* 4.2 15.2 - - + +
146D LEU* 4.0 33.0 - - + -
147D ILE* 4.9 2.3 - - - +
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Residues in contact with ILE 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D ILE* 4.1 10.8 - - + -
30D ILE* 3.6 37.7 - - + -
57D ILE* 4.0 18.0 - - + +
67D GLY* 3.7 18.4 - - - +
70D ILE* 3.7 41.1 - - + -
71D HIS* 4.3 6.7 - - - +
74D ILE* 3.9 12.7 - - + +
83D VAL* 4.8 1.4 - - - +
92D ALA 3.2 14.0 + - - +
93D GLY* 3.7 7.6 - - - +
95D THR* 1.3 75.5 - - - +
97D TYR* 1.3 66.4 + - - +
99D ALA* 3.0 20.6 + - - +
100D ALA 4.4 0.2 + - - -
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Residues in contact with TYR 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D ILE* 3.8 20.2 - - + -
83D VAL* 3.4 25.6 - - + +
85D GLY* 3.6 21.1 - - - -
89D VAL* 3.9 17.3 - - + -
93D GLY 2.9 18.3 + - - +
94D ILE* 3.2 5.4 + - + +
96D ILE* 1.3 77.2 - - - +
98D LEU* 1.3 60.9 + - + +
99D ALA 3.2 4.2 + - - -
100D ALA 3.6 3.6 + - - -
105D ARG* 3.4 31.4 - - + +
106D PHE 2.7 39.8 + - - -
113D TYR* 4.1 8.7 - + - -
178D ILE* 3.3 42.6 - - + -
179D VAL* 3.5 12.6 - - - +
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Residues in contact with LEU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D HIS* 4.5 4.8 + - - -
75D LYS* 4.9 3.8 + - - -
94D ILE* 2.9 38.0 + - + +
95D THR 3.9 5.8 - - - +
96D ILE 3.2 0.4 - - - -
97D TYR* 1.3 74.1 - - + +
99D ALA* 1.3 62.3 + - - +
100D ALA 3.2 9.2 - - - +
105D ARG* 3.6 34.9 + - - +
146D LEU* 4.7 6.1 - - + +
147D ILE* 3.8 38.4 - - + -
150D ALA* 3.8 23.1 - - + +
151D THR* 4.1 13.9 - - + -
178D ILE* 4.2 17.7 - - + -
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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