Contacts of the helix formed by residues 98 - 112 (chain A) in PDB entry 2JBO
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 CYS 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A GLN* 3.4 20.8 + - - +
97A ASP* 1.3 85.7 + - - +
99A PRO* 1.3 80.5 - - + +
100A LYS* 4.0 8.5 - - - -
101A ALA* 3.0 25.2 + - - +
102A ARG* 3.0 16.0 + - - +
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Residues in contact with PRO 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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98A CYS* 1.3 89.2 - - + +
100A LYS* 1.3 63.1 + - + +
102A ARG* 3.3 9.8 + - + +
103A ARG* 3.2 37.0 + - - +
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Residues in contact with LYS 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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98A CYS* 3.3 8.9 - - - -
99A PRO* 1.3 80.0 - - + +
101A ALA* 1.3 63.6 + - - +
103A ARG* 3.1 36.8 + - + +
104A GLU* 3.3 11.3 + - - +
209A GLY 5.5 5.8 - - - +
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Residues in contact with ALA 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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95A LEU* 4.1 20.9 - - + +
96A GLN 3.3 26.2 - - - +
98A CYS* 3.0 12.3 + - - +
100A LYS* 1.3 76.0 - - - +
102A ARG* 1.3 63.7 + - - +
103A ARG 3.2 0.2 + - - -
104A GLU* 3.3 6.9 + - - +
105A VAL* 3.1 25.5 + - - +
134A LEU* 3.9 16.8 - - + -
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Residues in contact with ARG 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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54A ILE* 3.7 28.7 - - - +
56A LYS* 5.7 0.2 - - - +
97A ASP* 3.1 36.9 + - - +
98A CYS 3.0 19.0 + - - +
99A PRO* 3.4 11.9 - - + +
101A ALA* 1.3 75.1 - - - +
103A ARG* 1.3 58.5 + - - +
105A VAL* 3.5 3.8 + - - +
106A GLU* 3.0 32.0 + - + +
125A GLU* 3.3 23.4 + - - +
132A LYS* 4.2 7.3 - - - +
134A LEU* 4.2 15.2 - - + +
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Residues in contact with ARG 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 PRO* 3.2 29.6 + - - +
100A LYS* 3.1 31.4 + - + +
102A ARG* 1.3 74.3 - - - +
104A GLU* 1.3 69.0 + - - +
106A GLU* 2.9 5.6 + - + -
107A LEU* 2.8 39.9 + - + +
211A ALA 6.0 0.7 - - - +
213A GLU* 4.3 19.1 - - - +
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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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93A LYS* 2.8 33.3 + - - +
95A LEU* 4.0 20.3 - - + +
100A LYS 3.3 7.7 + - - +
101A ALA* 3.5 10.4 - - - +
103A ARG* 1.3 79.6 - - - +
105A VAL* 1.3 66.0 + - - +
107A LEU* 3.7 4.8 - - - +
108A HIS* 2.8 28.3 + - + +
136A ILE* 4.4 5.8 - - + +
207A ASP* 5.1 0.2 - - - -
208A PHE* 3.7 27.2 + - + +
209A GLY* 3.0 33.1 + - - +
211A ALA 6.1 0.2 - - - -
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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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52A LEU* 4.0 22.2 - - + -
54A ILE* 5.6 2.5 - - + -
95A LEU* 4.7 2.0 - - + -
101A ALA 3.1 14.0 + - - +
102A ARG* 3.7 9.0 - - - +
104A GLU* 1.3 77.7 - - - +
106A GLU* 1.3 58.5 + - - +
108A HIS* 3.7 4.6 - - - +
109A TRP* 2.7 29.3 + - - +
120A ILE* 4.1 5.2 - - + +
123A VAL* 4.2 26.2 - - + -
134A LEU* 3.8 22.2 - - + -
136A ILE* 3.9 28.5 - - + -
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Residues in contact with GLU 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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52A LEU* 4.3 22.1 - - + +
102A ARG* 3.0 18.0 + - + +
103A ARG* 2.9 9.0 + - + +
105A VAL* 1.3 78.0 - - + +
107A LEU* 1.3 59.7 + - + +
109A TRP* 3.7 8.4 - - - +
110A ARG* 2.9 54.4 + - - +
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Residues in contact with LEU 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 ARG* 2.8 33.1 + - + +
104A GLU* 3.7 4.5 - - - +
106A GLU* 1.3 74.9 - - + +
108A HIS* 1.3 58.2 + - - +
110A ARG* 3.1 19.0 + - - +
111A ALA* 2.8 29.1 + - - +
182A ILE* 4.0 22.3 - - + +
208A PHE* 4.5 11.0 - - + -
211A ALA* 3.6 39.0 - - + +
212A LYS* 3.7 11.4 - - - +
213A GLU* 3.7 33.4 - - + +
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Residues in contact with HIS 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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104A GLU* 2.8 23.6 + - + +
105A VAL* 3.7 1.6 - - - +
107A LEU* 1.3 73.3 - - - +
109A TRP* 1.3 65.8 + - - +
111A ALA 3.2 0.3 + - - -
112A SER* 2.8 28.7 + - - -
117A ILE* 4.2 2.7 - - + +
118A VAL* 2.8 48.9 + - + +
120A ILE* 3.4 21.8 - - + +
136A ILE* 5.4 2.8 - - + +
138A MET* 3.9 22.5 - - + +
207A ASP 4.6 4.7 - - - -
208A PHE* 3.3 46.5 + + + +
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Residues in contact with TRP 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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50A SER* 3.3 33.4 + - - -
51A GLY* 3.3 16.5 - - - -
52A LEU* 3.4 52.7 - - + +
53A GLN 5.5 0.7 - - - -
105A VAL 2.7 21.2 + - - +
106A GLU* 3.7 8.7 - - - +
108A HIS* 1.3 70.7 - - - +
110A ARG* 1.3 74.4 + - + +
112A SER* 2.8 24.3 + - - -
113A GLN* 4.0 21.6 + - - +
120A ILE* 3.6 36.2 - - + +
121A VAL 5.4 6.3 - - - -
122A ASP* 5.7 2.0 - - - -
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Residues in contact with ARG 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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106A GLU* 2.9 34.2 + - - +
107A LEU* 3.3 26.0 - - - +
109A TRP* 1.3 85.7 - - + +
111A ALA* 1.3 58.1 + - - +
113A GLN* 4.1 14.8 + - - +
176A TYR* 4.2 4.9 + - - -
180A ILE* 3.7 44.3 + - + +
181A ASN* 5.0 2.0 + - - +
182A ILE* 4.1 19.0 - - + +
213A GLU* 4.4 13.7 + - - +
215A THR* 6.3 1.0 - - - +
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Residues in contact with ALA 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 LEU 2.8 17.8 + - - +
108A HIS 3.9 3.1 - - - +
109A TRP 3.1 0.4 - - - -
110A ARG* 1.3 70.4 - - - +
112A SER* 1.3 63.2 + - - +
113A GLN 2.9 8.4 + - - -
114A CYS* 2.9 20.7 + - - +
117A ILE* 3.9 10.1 - - + +
176A TYR* 4.2 8.3 - - + -
177A LEU* 3.7 30.5 - - + -
180A ILE* 4.5 1.6 - - + -
182A ILE* 4.8 2.5 - - + -
208A PHE* 4.0 15.7 - - + -
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Residues in contact with SER 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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108A HIS* 2.8 22.5 + - - -
109A TRP* 2.8 13.9 + - - -
111A ALA* 1.3 76.1 - - - +
113A GLN* 1.3 67.8 + - - +
114A CYS 3.1 9.1 + - - +
117A ILE* 4.4 5.1 - - - +
118A VAL 4.5 7.9 - - - -
119A ARG* 3.7 25.3 + - - +
120A ILE* 3.0 44.2 + - - +
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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