Contacts of the helix formed by residues 96 - 102 (chain A) in PDB entry 1OI4
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 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ASP 4.3 0.4 - - - -
33A GLU* 2.8 37.4 + - + -
67A LYS* 4.0 20.1 - - + -
95A GLY* 1.3 75.6 + - - -
97A SER* 1.3 65.3 + - - +
98A PRO* 3.4 1.6 - - - -
99A ASP* 3.3 12.6 + - + +
100A TYR* 3.3 25.6 + - + -
126A HIS* 5.4 3.6 + + - -
233B GLU* 4.3 2.4 + - - -
296B HIS* 3.1 55.3 + + + +
299B ASP* 3.8 22.6 + - - -
300B TYR* 3.1 26.7 + + - -
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Residues in contact with SER 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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29A LEU 4.3 1.7 + - - -
30A ILE* 3.7 4.7 - - - -
31A THR* 3.0 37.4 + - - +
32A ASP 3.9 2.5 - - - -
33A GLU 3.7 3.4 + - - -
34A PHE* 3.7 20.2 - - - -
93A PRO* 4.6 4.0 + - - +
94A GLY 3.6 9.4 - - - -
96A HIS* 1.3 77.5 - - - +
98A PRO* 1.3 71.0 - - - +
100A TYR* 3.1 4.3 + - - +
101A LEU* 3.0 30.9 + - - +
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Residues in contact with PRO 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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92A LEU* 6.0 0.2 - - + -
93A PRO 3.2 18.4 - - - +
94A GLY* 3.4 11.7 - - - +
95A GLY 3.7 6.5 - - - +
96A HIS 3.6 2.7 - - - -
97A SER* 1.3 96.5 - - - +
99A ASP* 1.3 56.7 - - - +
101A LEU* 4.4 0.4 - - + +
102A ARG* 2.8 37.8 + - - +
126A HIS 3.6 28.3 - - - +
127A GLY* 3.8 8.1 - - - +
129A GLN* 3.7 13.0 - - + +
130A LEU* 4.4 22.1 - - + +
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Residues in contact with ASP 99 (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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96A HIS* 3.3 18.3 + - + +
97A SER 3.2 0.8 - - - -
98A PRO* 1.3 80.4 - - - +
100A TYR* 1.3 81.1 + - - +
102A ARG* 3.5 13.3 + - - +
103A GLY 4.1 0.7 + - - -
129A GLN* 3.8 12.8 + - - +
296B HIS* 3.9 10.0 - - + -
326B HIS* 2.8 40.1 + - - -
329B GLN* 5.6 0.5 + - - -
347B PRO* 3.4 29.4 - - - +
348B ILE* 4.7 2.8 - - - +
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Residues in contact with TYR 100 (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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31A THR* 3.7 13.5 - - + -
32A ASP* 3.3 30.7 - - + -
33A GLU* 2.6 35.9 + - + -
58A LYS* 5.7 2.8 + - - -
96A HIS* 3.3 7.2 + - + -
97A SER 3.1 6.0 + - - +
99A ASP* 1.3 96.6 - - - +
101A LEU* 1.3 61.4 + - + +
103A GLY* 4.0 6.9 + - - -
104A ASP* 4.8 3.8 + - - +
267B LYS* 3.2 24.5 + - - -
296B HIS* 2.9 25.1 + + - -
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Residues in contact with LEU 101 (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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29A LEU* 3.7 37.5 - - + +
30A ILE* 3.8 4.0 - - - +
31A THR* 3.8 21.5 - - + +
57A GLU* 4.7 4.5 - - + -
58A LYS* 5.3 6.7 - - + -
97A SER* 3.0 34.1 + - - +
98A PRO 4.1 1.8 - - - +
100A TYR* 1.3 77.0 - - + +
102A ARG* 1.3 56.3 + - - +
103A GLY 3.0 11.0 + - - -
104A ASP* 3.1 25.5 + - - +
107A PHE* 3.7 44.2 - - + +
130A LEU* 4.2 13.5 - - + -
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Residues in contact with ARG 102 (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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98A PRO 2.8 28.8 + - - +
99A ASP* 3.5 20.3 + - - +
101A LEU* 1.3 71.8 - - - +
103A GLY* 1.3 56.8 + - - +
104A ASP 3.2 2.2 - - - -
108A VAL* 3.6 16.1 - - - +
129A GLN* 3.4 48.1 + - - +
130A LEU* 3.7 19.4 - - + +
132A ILE* 3.7 7.3 - - - +
133A SER* 2.9 35.1 + - - +
346B LYS 5.3 0.2 - - - +
347B PRO* 3.3 27.3 + - + +
348B ILE* 4.3 7.3 - - - +
350B ILE* 3.3 11.1 - - - +
351B ASP* 2.7 40.4 + - - -
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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