Contacts of the helix formed by residues 89 - 95 (chain H) in PDB entry 3DV0
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 VAL 89 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59H GLU* 3.6 25.4 - - + +
60H SER* 3.9 6.3 - - - +
63H GLY* 3.9 10.3 - - - -
80H ILE* 4.2 19.3 - - + -
85H PHE 4.4 2.7 - - - +
86H VAL* 2.7 25.0 + - + +
88H GLU* 1.3 80.7 - - - +
90H MET* 1.3 63.2 + - - +
91H ASP* 3.1 4.5 + - - +
92H SER* 3.2 28.5 + - - +
93H ILE* 3.3 29.6 + - + +
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Residues in contact with MET 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F TYR* 3.9 30.8 + - + +
90F MET* 3.7 41.3 - - + -
135F LEU* 4.2 20.6 - - + -
86H VAL* 3.0 33.7 + - - +
87H TYR* 3.7 7.2 + - + +
88H GLU 3.7 0.4 - - - -
89H VAL* 1.3 76.9 - - - +
91H ASP* 1.3 57.5 + - - +
93H ILE* 4.0 3.5 - - - +
94H CYS* 2.9 56.1 + - - +
95H GLY 3.7 0.2 + - - -
135H LEU* 4.5 17.3 - - + -
136H VAL* 5.1 5.4 - - - -
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Residues in contact with ASP 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F TYR* 3.5 26.3 + - + +
88F GLU* 3.0 29.9 - - - +
127F LEU* 5.0 0.3 - - - +
143G ILE* 3.6 20.4 - - - +
146G ALA* 3.6 10.9 - - - +
149G ILE* 5.9 0.9 - - - +
180G ASP* 4.4 7.3 - - - +
60H SER* 5.9 2.2 - - - +
89H VAL* 3.1 1.6 + - - +
90H MET* 1.3 77.2 - - - +
92H SER* 1.3 60.2 + - - +
95H GLY* 2.9 9.0 + - - -
96H GLN* 2.9 53.3 + - - +
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Residues in contact with SER 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149G ILE* 3.9 12.8 - - - +
150G GLN* 5.5 0.3 - - - +
60H SER* 4.7 1.9 + - - -
63H GLY* 3.4 13.7 - - - -
64H GLY* 3.2 22.3 + - - -
67H ILE* 3.6 8.8 - - - +
89H VAL* 3.2 24.8 + - - -
91H ASP* 1.3 79.0 + - - +
93H ILE* 1.3 57.9 + - - +
96H GLN* 3.4 10.7 - - - +
97H MET* 2.9 37.4 + - - +
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Residues in contact with ILE 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H ILE* 5.5 1.6 - - + -
83H PHE* 5.0 6.3 - - + -
86H VAL* 3.6 31.2 - - + -
89H VAL* 3.3 28.2 + - + +
90H MET* 4.0 2.9 - - - +
91H ASP 3.2 0.2 - - - -
92H SER* 1.3 77.8 - - - +
94H CYS* 1.3 68.3 + - - +
97H MET* 3.1 22.6 - - + +
98H ALA* 3.2 17.0 + - - +
114H ILE* 3.5 31.0 - - + -
136H VAL* 4.3 8.3 - - + -
142H LEU* 3.6 28.2 - - + +
168H ILE* 4.4 8.3 - - + -
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Residues in contact with CYS 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F TYR* 3.7 19.5 - - + +
135F LEU* 6.0 2.2 - - + -
90H MET* 2.9 35.6 + - - +
93H ILE* 1.3 90.7 - - - +
95H GLY* 1.3 61.8 + - - +
96H GLN 3.5 0.7 - - - -
98H ALA* 4.3 0.2 - - - +
99H ARG* 2.8 24.5 + - - +
135H LEU 5.3 0.7 - - - -
136H VAL* 4.4 11.4 - - - -
139H GLN* 3.3 41.5 - - + +
142H LEU* 4.1 3.6 - - - -
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Residues in contact with GLY 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F TYR* 3.5 21.7 - - - -
127F LEU* 4.1 6.8 - - - +
91H ASP* 2.9 20.3 + - - -
94H CYS* 1.3 75.6 - - - +
96H GLN* 1.3 65.7 + - - +
99H ARG* 3.5 13.4 - - - -
103H ARG* 2.8 24.6 + - - -
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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