Contacts of the strand formed by residues 91 - 100 (chain C) in PDB entry 1DVM
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 ILE 91 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82C LEU* 4.3 4.9 - - + +
83C MET* 3.0 34.8 - - + +
87C ASN* 2.7 46.2 + - + +
88C LYS* 4.1 3.1 - - - +
90C GLU* 1.3 76.1 - - - +
92C SER* 1.3 75.3 + - - +
93C THR* 3.7 15.5 - - + -
145C LYS* 3.8 6.6 + - - -
169C LEU* 4.8 0.2 - - + -
170C TYR* 3.3 16.6 - - - +
171C PHE* 3.9 15.3 - - + -
233C LEU* 5.5 0.2 - - + -
371C LEU* 5.3 12.6 - - + -
372C PHE* 3.4 28.7 - - + -
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Residues in contact with SER 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C MET* 4.4 4.9 - - - -
91C ILE* 1.3 76.1 + - - +
93C THR* 1.3 60.6 + - - +
143C HIS 4.4 3.9 + - - -
144C THR* 4.1 18.8 - - - +
145C LYS* 2.6 43.4 + - - +
168C ALA 4.0 0.5 - - - +
169C LEU* 3.4 1.6 - - - -
170C TYR* 2.7 55.4 + - - +
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Residues in contact with THR 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C TYR* 5.5 9.2 - - + -
79C TYR* 3.5 34.1 + - + -
82C LEU* 6.5 0.4 - - + -
83C MET* 3.7 20.1 - - + +
91C ILE* 3.7 15.9 - - + -
92C SER* 1.3 79.2 - - - +
94C THR* 1.3 66.1 + - - +
95C ASP* 5.4 2.9 + - - -
143C HIS* 3.6 11.3 + - - +
144C THR* 5.1 0.4 - - - -
168C ALA 3.5 6.5 - - - -
169C LEU* 3.5 33.7 - - + -
371C LEU* 6.2 1.6 - - + -
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Residues in contact with THR 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C TYR* 5.8 0.4 - - - -
93C THR* 1.3 80.1 + - - +
95C ASP* 1.3 62.2 + - - +
139C TRP* 2.9 30.4 + - + +
140C VAL* 4.1 22.2 - - + -
143C HIS* 3.2 21.7 + - + +
144C THR* 4.2 5.4 - - + -
166C VAL* 4.0 2.5 - - + +
167C ASN* 3.4 7.8 + - - -
168C ALA* 3.0 48.3 + - + +
169C LEU* 4.3 0.4 - - - +
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Residues in contact with ASP 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C GLY* 4.3 3.1 - - - +
41C SER* 3.5 22.5 + - - -
42C VAL* 3.2 21.1 - - + +
45C MET* 3.6 27.1 - - + +
79C TYR* 5.4 7.6 - - - -
93C THR* 5.4 2.3 + - - -
94C THR* 1.3 77.1 + - - +
96C ALA* 1.3 64.6 + - - +
122C LYS* 4.8 2.3 + - - -
139C TRP* 3.8 13.0 + - - -
166C VAL 3.7 4.5 - - - -
167C ASN* 2.7 32.7 + - - -
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Residues in contact with ALA 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C VAL* 4.5 1.6 - - - +
45C MET* 6.2 0.2 - - - -
94C THR* 6.1 0.2 - - + -
95C ASP* 1.3 77.1 - - - +
97C ILE* 1.3 67.6 + - - +
98C PHE* 3.4 30.1 - - + -
120C THR 5.5 0.4 - - - -
122C LYS* 4.3 7.4 - - - +
139C TRP* 3.5 24.7 - - + +
164C VAL 4.0 0.5 - - - +
165C LEU* 3.7 3.5 - - - +
166C VAL* 3.1 36.8 + - + +
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Residues in contact with ILE 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C VAL* 4.9 5.2 - - + +
45C MET* 4.1 37.0 - - + +
46C LEU* 4.3 18.2 - - + +
49C THR* 4.4 9.9 - - + -
96C ALA* 1.3 77.7 - - - +
98C PHE* 1.3 57.5 + - - +
113C PHE* 4.1 17.9 - - + -
120C THR 4.8 3.0 + - - +
121C VAL* 3.3 22.9 - - + +
122C LYS* 2.7 37.1 + - - +
163C LEU* 3.8 22.0 - - + -
164C VAL 3.5 10.8 - - - +
165C LEU* 5.1 9.4 - - + -
309C LEU* 5.7 0.2 - - + -
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Residues in contact with PHE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C ALA* 3.4 34.1 - - + -
97C ILE* 1.3 71.8 - - - +
99C VAL* 1.3 60.9 + - - +
122C LYS* 3.1 38.8 - - + +
124C VAL* 3.5 20.9 - - + -
126C PHE* 3.7 18.8 - - + -
135C ILE* 4.6 5.6 - - + -
136C ILE* 3.8 49.6 - - + -
139C TRP* 3.9 19.1 - + + -
140C VAL* 6.0 0.4 - - + -
163C LEU* 3.2 6.4 - - - +
164C VAL* 2.8 46.4 + - + -
166C VAL* 4.3 9.0 - - + -
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Residues in contact with VAL 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ILE 4.0 0.6 + - - -
98C PHE* 1.3 75.4 - - - +
100C GLN* 1.3 74.2 + - - +
103C LEU* 4.1 19.1 - - + -
105C LEU* 4.4 17.5 - - + -
121C VAL* 3.5 24.9 - - + -
122C LYS 2.8 6.7 + - - -
123C GLN* 3.1 24.4 - - + -
124C VAL 2.8 24.3 + - - -
126C PHE* 3.8 2.0 - - - -
162C ARG 3.2 11.7 - - - +
163C LEU* 4.1 8.7 - - + -
309C LEU* 4.2 19.7 - - + -
315C LEU* 4.7 1.8 - - + -
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Residues in contact with GLN 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C VAL* 1.3 79.5 - - - +
101C ARG* 1.3 65.0 + - - +
102C ASP* 3.3 36.8 + - + +
103C LEU* 3.3 31.2 + - + +
105C LEU* 5.2 0.5 - - - +
123C GLN* 4.5 1.7 + - - +
124C VAL 3.0 7.9 - - - -
125C ASP* 2.9 31.3 + - - +
126C PHE* 3.0 32.7 + - - +
127C SER* 4.3 4.5 + - - -
161C THR 3.8 0.2 - - - +
162C ARG* 2.8 50.5 + - - +
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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