Contacts of the helix formed by residues 98 - 112 (chain A) in PDB entry 2R0B
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 PHE 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A LEU* 4.1 17.9 - - + -
86A ASP 4.7 6.3 - - - -
87A ILE* 4.0 26.5 - - + -
94A ASN 4.6 2.7 - - - -
95A ILE 2.9 10.3 + - - +
97A ARG* 1.3 129.7 - - + +
99A PHE* 1.3 66.5 + - - +
100A PRO* 3.4 3.6 - - - -
101A MET* 3.1 43.9 + - + +
102A THR* 3.0 22.0 + - - +
130A PHE* 3.8 14.8 - - + -
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Residues in contact with PHE 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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95A ILE* 3.6 39.7 - - + -
96A ILE* 3.1 22.2 + - + +
98A PHE* 1.3 77.6 - - - +
100A PRO* 1.4 69.4 - - + +
102A THR* 3.3 4.8 + - - -
103A LYS* 3.0 25.5 + - - +
129A ALA 4.4 2.5 - - - -
130A PHE* 3.6 28.7 - + - -
133A ALA* 3.8 17.3 - - + -
166A GLN 3.9 16.2 - - - -
167A LEU* 3.7 27.8 - - + -
170A TYR* 3.5 43.2 + + + -
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Residues in contact with PRO 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 ILE 3.6 10.3 - - - +
97A ARG 3.9 8.3 - - - +
98A PHE 3.5 3.1 - - - -
99A PHE* 1.4 93.4 - - + +
101A MET* 1.3 60.4 + - - +
103A LYS* 3.7 4.6 - - + +
104A GLU* 3.0 25.8 + - - +
170A TYR* 4.0 22.4 - - + +
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Residues in contact with MET 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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83A LEU* 3.9 25.1 - - + -
85A LEU* 4.0 16.2 - - - -
97A ARG 5.3 2.4 + - - +
98A PHE* 3.1 47.5 + - + +
100A PRO* 1.3 79.3 - - - +
102A THR* 1.3 58.3 + - + +
104A GLU* 3.4 15.3 + - - +
105A PHE* 3.0 27.5 + - - +
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Residues in contact with THR 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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61A ILE* 3.9 16.2 - - + -
83A LEU* 4.0 12.6 - - + -
85A LEU* 3.7 22.7 - - + -
98A PHE* 3.0 12.5 + - + +
99A PHE* 3.3 10.6 + - - -
101A MET* 1.3 73.9 - - + +
103A LYS* 1.3 62.6 + - - +
105A PHE* 3.6 6.3 - - - +
106A ILE* 2.9 39.9 + - - +
130A PHE* 3.4 37.1 + - + +
133A ALA* 5.7 1.2 - - - +
134A TYR* 6.2 0.3 - - - +
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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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99A PHE 3.0 18.0 + - - +
100A PRO* 3.7 6.3 - - + +
102A THR* 1.3 77.4 + - - +
104A GLU* 1.3 58.0 + - - +
106A ILE* 3.9 0.7 - - - +
107A ASP* 2.8 67.7 + - - +
134A TYR* 3.8 25.5 - - + +
137A GLU* 4.1 35.9 - - + +
138A THR* 2.8 33.0 + - - +
170A TYR* 5.0 1.1 - - + +
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Residues in contact with GLU 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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100A PRO 3.0 16.3 + - - +
101A MET* 3.6 13.3 - - - +
103A LYS* 1.3 76.4 - - - +
105A PHE* 1.3 57.0 + - - +
107A ASP* 3.4 6.4 + - - +
108A GLY* 2.9 27.9 + - - -
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Residues in contact with PHE 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 HIS* 3.7 35.2 - + + -
60A ILE 4.1 4.9 - - - -
61A ILE* 3.5 35.0 - - + -
81A ARG* 3.6 26.0 - - + -
82A TYR 4.0 8.1 - - - -
83A LEU* 3.9 36.1 - - + -
101A MET* 3.0 17.7 + - + +
102A THR 3.6 4.0 - - - +
104A GLU* 1.3 77.0 - - - +
106A ILE* 1.3 66.3 + - + +
108A GLY* 3.4 1.4 + - - -
109A SER* 3.1 22.7 + - - -
116A VAL* 4.5 2.7 - - + -
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Residues in contact with ILE 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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36A LEU* 4.1 20.4 - - + -
61A ILE* 4.1 17.9 - - + -
102A THR* 2.9 25.5 + - - +
103A LYS 4.0 0.2 - - - +
105A PHE* 1.3 73.8 - - - +
107A ASP* 1.3 65.0 + - - +
109A SER* 3.3 2.6 + - - -
110A LEU* 3.0 37.2 + - + +
116A VAL* 4.1 27.4 - - + -
118A VAL* 4.5 4.9 - - + -
130A PHE* 5.1 5.2 - - + +
131A VAL* 5.9 0.4 - - - -
134A TYR* 3.4 52.5 - - + -
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Residues in contact with ASP 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* 2.8 62.3 + - - +
104A GLU* 3.8 5.7 - - - +
106A ILE* 1.3 76.8 - - - +
108A GLY* 1.3 55.9 + - - +
110A LEU* 4.1 3.7 - - - +
111A GLN* 2.9 34.9 + - - +
134A TYR* 3.3 18.4 + - - -
138A THR* 5.2 0.3 - - - +
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Residues in contact with GLY 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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59A HIS* 5.2 0.2 - - - -
104A GLU 2.9 17.1 + - - -
105A PHE* 3.8 1.6 - - - -
107A ASP* 1.3 77.2 - - - +
109A SER* 1.3 63.5 + - - +
111A GLN* 3.9 5.5 - - - +
112A MET* 3.5 28.9 + - - +
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Residues in contact with SER 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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59A HIS* 3.0 41.9 + - - -
105A PHE 3.1 9.1 + - - -
106A ILE 3.6 2.2 - - - -
108A GLY* 1.3 77.9 - - - +
110A LEU* 1.3 61.1 + - - +
112A MET* 3.1 11.6 + - - +
114A GLY 2.9 40.6 + - - -
115A LYS 3.4 0.5 + - - -
116A VAL* 3.4 26.8 - - - +
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Residues in contact with LEU 110 (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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33A LEU* 4.8 6.3 - - + -
34A PRO 4.2 14.4 - - - +
35A GLY* 3.5 30.5 - - - +
36A LEU* 5.1 1.6 - - + -
106A ILE* 3.0 26.0 + - + +
107A ASP* 4.1 4.3 - - - +
109A SER* 1.3 80.0 - - - +
111A GLN* 1.3 62.3 + - - +
113A GLY* 3.2 12.6 + - - -
114A GLY 3.3 20.6 - - - +
115A LYS* 4.2 3.4 - - - -
116A VAL* 4.3 6.3 - - + -
134A TYR* 3.7 26.0 - - + +
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Residues in contact with GLN 111 (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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107A ASP 2.9 18.1 + - - +
108A GLY* 3.9 7.2 - - - +
109A SER 3.2 0.2 - - - -
110A LEU* 1.3 79.5 - - - +
112A MET* 1.3 56.0 + - - +
113A GLY 3.2 2.8 + - - -
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Residues in contact with MET 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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58A THR* 5.8 0.2 - - - -
59A HIS* 4.1 21.8 - - + +
81A ARG* 4.0 27.1 - - - +
108A GLY* 3.5 17.6 + - - +
109A SER* 3.1 20.1 + - - +
111A GLN* 1.3 76.7 - - - +
113A GLY* 1.3 57.9 + - - +
114A GLY* 3.6 6.2 + - - +
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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