Contacts of the helix formed by residues 91 - 98 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60F GLN 3.9 12.6 + - - -
61F GLY* 4.3 2.5 - - - -
62F GLY 5.2 0.9 - - - -
90F ALA* 1.3 75.4 - - - +
92F ALA* 1.3 60.1 + - - -
94F ILE* 2.9 17.9 + - - +
95F THR* 3.3 5.7 + - - -
114F MET* 3.0 17.5 + - - +
116F HIS* 2.7 33.6 + - - -
117F GLN* 3.1 23.3 + - - +
118F PRO* 4.1 17.3 - - - +
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Residues in contact with ALA 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ILE* 4.3 9.6 - - + -
61F GLY* 3.9 1.5 - - - -
62F GLY 3.8 25.1 - - - +
63F HIS 4.3 18.2 - - - +
64F VAL* 4.9 5.4 - - - -
67F GLY* 4.6 5.8 - - - -
90F ALA 3.2 0.4 + - - -
91F SER* 1.3 79.1 - - - +
93F GLY* 1.3 61.0 + - - +
95F THR* 3.3 12.2 + - - -
96F ILE* 3.2 28.3 + - - +
117F GLN* 3.8 4.7 + - - +
118F PRO* 5.4 0.6 - - - +
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Residues in contact with GLY 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ILE* 4.3 0.4 - - - +
57F ILE* 4.4 5.2 - - - +
59F SER* 4.5 18.8 - - - -
61F GLY* 3.8 4.4 - - - -
89F VAL* 3.5 12.9 - - - +
90F ALA 2.8 13.2 + - - -
92F ALA* 1.3 78.2 - - - +
94F ILE* 1.3 56.2 + - - +
96F ILE* 3.5 12.0 + - - +
97F TYR* 2.9 28.4 + - - +
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Residues in contact with ILE 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F VAL* 3.5 24.2 - - + +
90F ALA* 3.6 2.9 + - - -
91F SER 2.9 12.2 + - - +
93F GLY* 1.3 74.1 - - - +
95F THR* 1.3 59.1 - - - +
97F TYR* 3.2 3.0 + - + +
98F LEU* 2.9 49.6 + - + +
113F TYR* 3.8 24.9 - - + -
114F MET 3.3 24.5 - - - +
115F ILE* 4.0 24.5 - - + -
117F GLN* 4.4 1.1 - - - +
147F ILE* 4.4 11.7 - - + -
178F ILE* 4.1 16.2 - - + -
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Residues in contact with THR 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F GLY 4.7 5.8 - - - +
68F ASP* 4.4 13.9 - - - +
71F HIS* 3.1 33.6 - - + -
91F SER 3.3 9.6 + - - -
92F ALA* 3.3 12.3 + - - -
94F ILE* 1.3 80.3 - - - +
96F ILE* 1.3 60.7 + - - +
98F LEU* 3.4 8.9 + - - +
99F ALA 3.5 0.2 + - - -
117F GLN* 4.0 14.4 + - - -
143F ILE* 4.2 14.9 - - + +
146F LEU* 4.0 33.2 - - + +
147F ILE* 4.9 2.2 - - - +
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Residues in contact with ILE 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F ILE* 4.1 10.1 - - + -
30F ILE* 3.6 36.8 - - + -
57F ILE* 3.9 18.7 - - + +
67F GLY* 3.7 19.3 - - - +
70F ILE* 3.7 41.1 - - + -
71F HIS* 4.3 6.5 - - - +
74F ILE* 3.9 12.9 - - + +
83F VAL* 4.8 1.4 - - - +
92F ALA 3.2 14.0 + - - +
93F GLY* 3.7 8.1 - - - +
94F ILE 3.3 0.2 - - - -
95F THR* 1.3 73.4 - - - +
97F TYR* 1.3 66.3 + - - +
99F ALA* 3.0 20.4 + - - +
100F ALA 4.4 0.3 + - - -
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Residues in contact with TYR 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F ILE* 3.8 20.9 - - + -
83F VAL* 3.4 25.9 - - + +
85F GLY* 3.6 21.5 - - - -
89F VAL* 3.9 16.4 - - + -
93F GLY 2.9 18.7 + - - +
94F ILE* 3.5 4.9 - - + +
96F ILE* 1.3 76.6 - - - +
98F LEU* 1.3 61.4 - - + +
99F ALA 3.2 4.3 + - - -
100F ALA 3.5 3.8 + - - -
105F ARG* 3.4 31.5 - - + +
106F PHE 2.7 39.6 + - - -
113F TYR* 4.1 7.9 - + - -
178F ILE* 3.3 42.8 - - + -
179F VAL* 3.6 12.5 - - - +
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Residues in contact with LEU 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F HIS* 4.5 4.6 + - - -
75F LYS* 4.9 3.6 + - - -
94F ILE* 2.9 38.1 + - + +
95F THR 3.9 6.5 - - - +
96F ILE 3.2 0.4 - - - -
97F TYR* 1.3 75.4 - - + +
99F ALA* 1.3 62.8 + - - +
100F ALA 3.3 8.9 - - - +
105F ARG* 3.6 35.2 + - - +
146F LEU* 4.7 5.5 - - + +
147F ILE* 3.8 37.7 - - + -
150F ALA* 3.8 22.9 - - + +
151F THR* 4.0 15.3 - - + -
178F 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