Contacts of the helix formed by residues 91 - 96 (chain A) in PDB entry 5OO2
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 GLY 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A HIS* 6.1 0.2 - - - -
81A PHE* 3.9 9.6 - - - -
88A TYR 3.7 16.3 + - - -
89A PHE* 3.7 6.5 - - - +
90A PRO* 1.3 74.7 - - - +
92A PRO* 1.3 77.5 - - - +
93A ALA 3.0 4.7 + - - -
94A ARG* 3.0 12.7 + - - +
95A TRP* 3.3 10.0 + - - -
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Residues in contact with PRO 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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38A HIS* 5.7 0.4 - - - +
81A PHE* 3.5 46.6 - - + -
85A VAL 5.4 7.4 - - - +
86A ASP* 5.8 3.4 - - - +
91A GLY* 1.3 83.5 - - - +
93A ALA* 1.3 56.6 + - - +
95A TRP* 3.5 3.6 + - + +
96A ALA* 2.9 26.7 + - - -
97A THR* 4.6 1.4 + - - -
98A ALA* 5.7 0.7 + - - +
109A LEU* 4.1 31.4 - - + -
110A THR 5.3 1.8 - - - +
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Residues in contact with ALA 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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91A GLY 3.0 1.4 + - - -
92A PRO* 1.3 78.0 - - - +
94A ARG* 1.3 67.8 + - - +
96A ALA* 3.5 15.5 + - - +
233A LYS* 4.9 1.2 + - - -
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Residues in contact with ARG 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 PHE* 3.8 27.1 - - + -
90A PRO* 3.7 26.2 - - + -
91A GLY 3.0 10.1 + - - +
93A ALA* 1.3 79.5 - - - +
95A TRP* 1.3 59.3 + - - +
199A LEU* 4.2 11.1 - - - +
200A PRO* 2.6 48.1 + - - +
201A GLU 3.1 20.6 + - - -
202A TYR* 4.1 12.7 - - - +
226A LEU* 4.1 15.2 + - + +
229A LEU* 4.3 7.2 - - + +
230A GLU* 4.4 7.6 + - - +
233A LYS* 2.8 38.0 + - - +
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Residues in contact with TRP 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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78A HIS* 3.7 19.3 - + - -
79A ILE* 4.6 4.0 - - + +
81A PHE* 3.6 20.0 - + - -
90A PRO* 3.3 25.0 + - + +
91A GLY 3.3 20.9 + - - -
92A PRO 3.9 6.1 - - - +
94A ARG* 1.3 77.7 - - - +
96A ALA* 1.3 67.1 + - - +
97A THR* 3.0 7.0 + - + +
110A THR 4.3 10.1 - - - +
111A SER* 3.6 8.3 - - - -
112A GLY* 3.4 23.3 - - - -
113A ILE* 3.6 35.4 - - + -
177A TRP* 4.0 12.8 - + - -
229A LEU* 3.4 42.2 - - + -
232A MET* 4.8 1.3 - - - -
233A LYS* 3.2 6.2 - - - +
237A TYR* 2.7 43.8 + + - +
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Residues in contact with ALA 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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92A PRO 2.9 16.2 + - - -
93A ALA* 3.7 12.8 - - - +
94A ARG 3.3 3.5 - - - +
95A TRP* 1.3 76.9 - - - +
97A THR* 1.3 58.9 + - - +
98A ALA* 3.3 3.8 - - - +
99A THR* 3.2 15.7 + - + +
100A LEU* 2.9 44.0 + - + +
233A LYS* 4.2 5.6 - - + +
237A TYR* 4.7 0.2 - - - -
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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