Contacts of the helix formed by residues 100 - 113 (chain A) in PDB entry 2P02
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ALA 4.2 1.0 + - - -
99A VAL* 1.3 71.8 - - - +
101A TYR* 1.3 61.8 + - - +
102A GLN* 3.3 13.3 + - - +
103A LYS* 3.2 37.9 + - + +
104A VAL* 3.0 25.8 + - + +
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Residues in contact with TYR 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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63A VAL* 3.8 25.8 - - + -
67A HIS* 2.9 25.5 + - - -
89A LEU* 3.7 27.4 - - + -
93A ILE* 3.6 11.4 - - - +
99A VAL* 3.4 29.0 + - + -
100A ASP* 1.3 69.1 + - - +
102A GLN* 1.3 66.6 + - + +
104A VAL* 4.5 3.1 - - - +
105A VAL* 2.9 31.0 + - + +
128A VAL* 4.8 1.3 - - - -
130A VAL* 4.1 26.7 - - + -
132A LEU* 3.6 22.8 - - + +
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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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100A ASP* 3.3 10.2 + - - +
101A TYR* 1.3 77.8 - - + +
103A LYS* 1.3 63.6 + - - +
105A VAL* 4.0 0.7 - - - +
106A ARG* 2.9 68.4 + - - +
128A VAL* 3.2 37.7 + - - +
130A VAL* 5.4 4.4 - - - +
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Residues in contact with LYS 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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100A ASP* 3.2 31.3 + - + +
102A GLN* 1.3 77.8 - - - +
104A VAL* 1.3 69.0 + - + +
106A ARG* 4.8 3.4 - - - +
107A GLU* 2.9 45.2 + - + +
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Residues in contact with VAL 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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59A ILE* 6.1 0.2 - - + -
62A ALA* 3.7 39.3 - - + +
63A VAL* 3.9 15.5 - - + +
66A ALA* 3.9 11.9 - - + -
99A VAL* 3.9 18.8 - - + -
100A ASP* 3.0 21.7 + - + +
101A TYR* 4.0 5.4 - - - +
103A LYS* 1.3 79.4 - - + +
105A VAL* 1.3 64.2 + - - +
107A GLU* 3.5 4.2 + - - +
108A ALA* 3.2 22.5 + - - +
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Residues in contact with VAL 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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59A ILE* 3.9 29.8 - - + -
63A VAL* 4.9 4.5 - - + -
87A ILE* 3.7 30.3 - - + -
89A LEU* 4.0 23.6 - - + -
101A TYR 2.9 20.9 + - - +
102A GLN 4.0 1.6 - - - +
104A VAL* 1.3 76.9 - - - +
106A ARG* 1.3 65.5 + - + +
108A ALA* 3.2 4.6 + - - +
109A VAL* 3.1 23.9 + - + +
126A CYS* 5.5 0.7 - - - -
128A VAL* 3.8 26.9 - - + -
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Residues in contact with ARG 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 49.4 + - - +
103A LYS* 4.1 3.1 - - - +
105A VAL* 1.3 77.2 - - + +
107A GLU* 1.3 58.7 + - + +
109A VAL* 3.3 1.6 + - - -
110A LYS* 2.9 27.0 + - - +
123A TYR* 2.9 55.2 + - + +
124A LYS* 3.6 13.0 + - - +
125A THR 4.1 0.4 - - - -
126A CYS* 2.8 39.1 + - - +
127A ASN* 4.6 0.4 - - - +
128A VAL* 3.7 20.6 - - + +
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Residues in contact with GLU 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 LYS* 2.9 37.8 + - + +
104A VAL* 4.0 3.8 - - - +
106A ARG* 1.3 77.9 - - + +
108A ALA* 1.3 62.2 + - - +
110A LYS* 3.4 13.8 + - + +
111A HIS* 3.0 23.9 + - - +
123A TYR* 5.5 0.2 - - - -
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Residues in contact with ALA 108 (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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58A GLN* 5.1 1.1 - - + -
59A ILE* 4.0 21.8 - - + +
62A ALA* 4.2 10.8 - - + -
104A VAL 3.2 12.7 + - - +
105A VAL 3.2 9.3 + - - +
107A GLU* 1.3 77.2 - - - +
109A VAL* 1.3 60.6 + - - +
111A HIS* 3.3 6.1 + - - +
112A ILE* 3.2 30.7 + - + +
394A GLN* 4.0 23.9 + - - +
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Residues in contact with VAL 109 (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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55A ILE* 4.6 9.6 - - + -
59A ILE* 3.9 23.3 - - + -
87A ILE* 4.6 8.7 - - + -
105A VAL* 3.1 22.2 + - + +
106A ARG* 4.9 0.2 - - - -
108A ALA* 1.3 72.9 - - - +
110A LYS* 1.3 65.3 + - - +
112A ILE* 3.2 10.3 + - + +
113A GLY 3.2 16.5 + - - -
114A TYR* 3.4 37.3 + - + +
121A PHE* 3.9 18.8 - - + -
123A TYR* 3.7 17.0 - - + -
126A CYS* 5.5 1.3 - - - -
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Residues in contact with LYS 110 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A ARG 2.9 17.4 + - - +
107A GLU* 3.5 13.7 - - + +
109A VAL* 1.3 76.1 - - - +
111A HIS* 1.3 64.6 + - - +
113A GLY* 3.1 15.4 + - - -
114A TYR 4.7 1.3 - - - +
115A ASP* 5.5 1.7 - - + +
123A TYR* 3.6 51.5 + - + +
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Residues in contact with HIS 111 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLU* 4.1 17.3 + - - -
58A GLN* 5.0 5.4 - - - -
107A GLU 3.0 13.7 + - - +
108A ALA* 3.3 11.9 + - - +
110A LYS* 1.3 76.8 - - - +
112A ILE* 1.3 66.0 + - + +
113A GLY* 3.4 1.0 + - - -
191A ARG* 3.0 28.4 + - - -
394A GLN* 5.0 11.9 - - - +
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Residues in contact with ILE 112 (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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49A GLU* 3.5 22.9 - - + +
50A GLY* 3.6 18.6 - - - +
55A ILE* 4.1 24.9 - - + +
58A GLN* 3.6 42.8 - - + +
59A ILE* 5.5 0.7 - - + -
108A ALA* 3.2 20.7 + - + +
109A VAL* 3.5 9.9 - - - +
110A LYS 3.2 0.2 - - - -
111A HIS* 1.3 78.5 - - + +
113A GLY* 1.3 57.7 + - - +
114A TYR* 4.1 16.4 - - + -
190A ARG* 3.1 28.6 + - - -
191A ARG* 4.0 5.8 - - - +
200A PRO* 3.7 2.9 - - + +
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Residues in contact with GLY 113 (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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109A VAL 3.2 1.0 + - - -
110A LYS 3.1 15.2 + - - -
111A HIS 4.3 1.1 - - - -
112A ILE* 1.3 79.2 - - - +
114A TYR* 1.3 60.2 + - - +
115A ASP* 3.2 20.1 + - - +
119A LYS* 3.7 15.8 + - - +
190A ARG* 4.0 12.1 + - - -
200A PRO* 4.0 9.3 - - - +
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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