Contacts of the helix formed by residues 97 - 107 (chain A) in PDB entry 3C0M
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 ASP 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A GLY* 1.3 77.8 - - - -
98A GLU* 1.3 67.0 + - - +
99A VAL* 3.3 9.4 - - + +
100A ASP* 2.9 37.9 + - - +
101A VAL* 3.1 6.5 + - - +
233A TYR* 4.4 8.4 - - - -
234A GLY* 3.5 20.1 + - - -
235A LEU 4.2 4.9 - - - +
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Residues in contact with GLU 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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96A GLY 3.9 0.6 + - - -
97A ASP* 1.3 73.0 - - - +
99A VAL* 1.3 64.9 + - - +
101A VAL* 2.9 5.1 + - - +
102A GLN* 2.9 37.3 + - - +
175A PHE* 4.7 2.3 - - - +
177A TYR* 2.4 42.6 + - + +
234A GLY 4.8 1.4 - - - -
235A LEU* 3.9 25.3 - - + +
238A LYS* 3.2 37.4 - - + +
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Residues in contact with VAL 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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97A ASP* 4.5 7.6 - - + +
98A GLU* 1.3 79.7 - - - +
100A ASP* 1.3 79.4 + - - +
102A GLN* 4.4 6.5 - - - +
103A TRP* 2.8 34.7 + - + +
144A ARG* 4.2 23.3 - - - +
149A TRP* 4.3 19.1 - - + -
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Residues in contact with ASP 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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96A GLY* 3.9 4.2 - - - -
97A ASP* 2.9 48.5 + - - +
99A VAL* 1.3 88.2 - - - +
101A VAL* 1.3 57.4 + - - +
103A TRP* 3.8 5.4 - - - +
104A ARG* 3.1 55.2 + - - +
233A TYR* 5.8 0.5 - - - -
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Residues in contact with VAL 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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93A ILE* 4.2 25.4 - - + +
94A PRO 4.4 16.2 - - - +
95A ASP 5.0 0.2 - - - -
96A GLY 4.5 6.5 - - - +
97A ASP 3.1 12.3 + - - +
98A GLU* 2.9 9.0 + - - +
100A ASP* 1.3 74.6 - - - +
102A GLN* 1.3 69.3 + - + +
104A ARG* 3.3 4.0 + - - +
105A LEU* 3.1 22.6 + - + +
177A TYR* 4.9 13.0 - - + -
235A LEU* 3.9 26.5 - - + -
312A VAL* 5.1 9.0 - - + -
398A ALA* 4.7 11.4 - - + -
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Residues in contact with GLN 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 GLU* 2.9 34.1 + - - +
99A VAL* 3.9 4.7 - - - +
101A VAL* 1.3 77.4 - - + +
103A TRP* 1.3 66.8 + - - +
105A LEU* 2.9 7.0 + - - -
106A VAL* 2.9 29.6 + - - +
144A ARG* 4.0 6.3 + - - +
147A ASP 3.8 8.2 + - - +
149A TRP* 2.5 43.5 + - + +
175A PHE* 3.7 37.2 - - + +
177A TYR* 3.3 23.8 + - - +
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Residues in contact with TRP 103 (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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99A VAL* 2.8 28.9 + - + +
100A ASP* 3.8 5.8 - - - +
102A GLN* 1.3 72.8 - - - +
104A ARG* 1.3 73.3 + - + +
106A VAL* 4.9 0.9 - - - -
107A HIS* 3.0 78.7 + + + +
149A TRP* 3.7 27.4 - + + -
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Residues in contact with ARG 104 (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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93A ILE* 4.0 19.8 - - + +
94A PRO* 2.3 59.0 + - - +
95A ASP 3.5 11.5 + - - -
96A GLY* 4.6 1.8 - - - +
100A ASP* 3.1 39.2 + - - +
101A VAL 3.8 4.4 - - - +
102A GLN 3.3 0.2 - - - -
103A TRP* 1.3 83.9 - - + +
105A LEU* 1.3 60.9 + - - +
107A HIS* 4.5 1.2 - - - -
108A ASP* 3.6 19.9 + - - +
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Residues in contact with LEU 105 (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 LEU* 4.9 9.0 - - + -
93A ILE* 4.9 13.4 - - + +
101A VAL* 3.1 12.8 + - + +
102A GLN* 2.9 10.1 + - - +
104A ARG* 1.3 76.4 - - - +
106A VAL* 1.3 66.7 + - + +
108A ASP* 3.3 19.8 + - + +
111A ASN* 5.8 0.9 - - + +
112A PHE* 3.5 37.2 - - + +
175A PHE* 4.2 20.0 - - + -
312A VAL* 5.1 3.4 - - + -
314A TYR* 3.8 28.0 - - + -
396A VAL* 4.2 31.9 - - + -
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Residues in contact with VAL 106 (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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102A GLN* 2.9 22.2 + - + +
103A TRP* 4.1 1.3 - - - +
105A LEU* 1.3 76.8 - - + +
107A HIS* 1.3 62.2 + - - +
108A ASP 3.3 0.9 - - - -
112A PHE* 4.4 8.2 - - + -
113A ILE* 3.3 22.2 - - - +
142A VAL* 3.4 27.9 - - + +
149A TRP* 3.9 39.7 - - + -
151A ILE* 3.8 18.5 - - + +
172A VAL* 5.0 8.3 - - + -
175A PHE* 4.7 9.0 - - + -
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Residues in contact with HIS 107 (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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103A TRP* 3.0 86.4 + + + +
104A ARG* 4.5 2.0 - - - +
106A VAL* 1.3 77.7 - - + +
108A ASP* 1.3 59.5 + - - +
109A SER* 3.2 9.3 + - - -
113A ILE* 3.7 9.6 - - - +
142A VAL* 3.7 40.3 + - + +
149A TRP* 4.1 8.7 - + - -
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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