Contacts of the helix formed by residues 97 - 110 (chain A) in PDB entry 1B43
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 ARG 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A ARG* 4.6 17.0 - - - +
94A ARG* 2.7 29.8 + - - +
95A GLU* 3.1 20.1 + - - +
96A ALA* 1.3 77.3 - - - +
98A GLU* 1.3 60.3 + - - +
99A GLU* 3.2 3.4 - - - +
100A ALA* 3.1 30.7 + - + +
122A ARG 5.7 0.4 - - - -
123A ALA* 3.8 34.1 - - + +
124A THR* 5.3 3.0 - - - +
125A ARG* 3.2 38.8 - - - +
132B GLU* 5.5 5.3 + - - -
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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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95A GLU 3.5 9.4 - - - +
96A ALA* 2.7 15.8 - - - +
97A ARG* 1.3 86.4 + - - +
99A GLU* 1.3 62.7 + - - +
100A ALA 3.0 6.6 + - - -
101A GLU* 4.2 9.3 + - - +
102A GLU* 4.3 11.6 + - - +
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Residues in contact with GLU 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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96A ALA* 2.7 31.4 - - - +
97A ARG* 3.2 0.8 - - - -
98A GLU* 1.3 80.0 - - - +
100A ALA* 1.3 58.0 + - - +
101A GLU 3.2 6.4 + - - -
103A LYS* 3.0 47.7 + - + +
104A TRP* 3.2 6.4 + - - +
119A TYR* 4.5 9.0 - - + +
122A ARG* 5.3 17.8 + - - +
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Residues in contact with ALA 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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97A ARG* 3.1 20.5 + - + +
98A GLU 3.0 1.2 - - - -
99A GLU* 1.3 76.7 - - - +
101A GLU* 1.3 72.1 + - - +
104A TRP* 4.6 6.5 - - - -
119A TYR 4.2 7.4 - - - +
122A ARG 4.4 1.6 - - - +
123A ALA* 3.0 39.0 - - + +
126A VAL* 4.0 12.5 - - + +
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Residues in contact with GLU 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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98A GLU* 4.5 6.3 - - - +
99A GLU 3.2 2.6 + - - -
100A ALA* 1.3 81.2 - - - +
102A GLU* 1.3 72.1 + - + +
104A TRP* 4.1 6.5 - - - +
105A ARG* 3.0 33.0 + - - +
125A ARG 5.2 2.1 - - - +
126A VAL* 4.4 20.0 - - - +
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Residues in contact with GLU 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 4.3 8.7 + - - +
99A GLU 4.1 0.4 + - - -
101A GLU* 1.3 87.9 - - + +
103A LYS* 1.3 58.9 + - + +
104A TRP 3.3 1.3 - - - -
105A ARG* 3.7 7.3 - - - +
106A GLU* 2.7 39.1 + - + +
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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 GLU* 3.0 41.1 + - + +
102A GLU* 1.3 76.1 - - + +
104A TRP* 1.3 63.5 + - - +
106A GLU* 3.2 23.0 + - + +
107A ALA 3.1 17.0 + - - -
119A TYR* 3.2 36.8 + - + -
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Residues in contact with TRP 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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32A TYR* 3.0 20.9 + - - -
99A GLU 3.2 3.8 + - - +
100A ALA* 4.6 1.3 - - - -
101A GLU* 4.1 10.5 - - - +
102A GLU 3.3 0.4 - - - +
103A LYS* 1.3 77.1 - - - +
105A ARG* 1.3 83.1 + - + +
106A GLU 3.2 0.3 + - - -
107A ALA* 3.2 4.9 + - - +
108A LEU* 3.1 56.9 + - + +
116A ALA* 3.0 33.9 + - + +
119A TYR* 3.8 15.7 - - + -
120A ALA* 3.4 13.3 - - + +
126A VAL* 3.3 51.4 - - + -
127A ASN* 3.3 19.7 - - - -
130A LEU* 3.9 27.1 - - + -
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Residues in contact with ARG 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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51A GLY 3.8 11.3 + - - -
52A ARG* 4.1 10.7 - - - +
53A ILE* 3.8 37.2 - - - +
101A GLU* 3.0 26.5 + - - +
102A GLU* 3.9 9.9 - - - +
103A LYS 3.4 0.4 - - - -
104A TRP* 1.3 90.3 - - + +
106A GLU* 1.3 55.0 + - - +
108A LEU* 4.0 14.3 - - - +
109A GLU* 2.6 67.8 + - + +
130A LEU* 6.1 3.2 - - - +
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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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102A GLU* 2.7 24.0 + - + +
103A LYS* 3.2 31.4 + - + +
105A ARG* 1.3 78.8 - - - +
107A ALA* 1.3 60.7 + - - +
109A GLU* 4.6 2.3 - - - +
110A LYS* 3.1 62.5 + - - +
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Residues in contact with ALA 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 3.1 14.5 + - - +
104A TRP 3.2 0.4 + - - -
106A GLU* 1.3 76.6 - - - +
108A LEU* 1.3 57.5 + - - +
110A LYS* 5.2 0.4 - - - -
111A GLY 3.2 19.9 + - - +
112A GLU 2.9 33.9 + - - +
115A GLU* 3.7 13.0 - - + -
116A ALA* 3.5 26.5 - - + +
119A TYR* 4.5 3.1 - - + -
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Residues in contact with LEU 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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32A TYR* 5.1 1.1 - - + +
35A LEU* 3.9 29.8 - - + -
45A PRO* 3.9 13.9 - - - +
53A ILE* 3.6 26.7 - - + -
104A TRP* 3.1 64.2 + - + +
105A ARG* 3.5 15.3 - - - +
107A ALA* 1.3 74.4 - - - +
109A GLU* 1.3 55.7 + - - +
110A LYS 2.6 16.9 + - - -
111A GLY* 3.3 12.3 + - - +
113A ILE* 4.9 14.1 - - + +
116A ALA* 4.2 11.9 - - + -
130A LEU* 5.4 3.1 - - + -
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Residues in contact with GLU 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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44A THR* 5.4 1.9 - - - +
45A PRO* 5.0 4.8 - - - +
47A MET* 4.2 23.1 - - - +
51A GLY* 3.8 11.0 - - - +
53A ILE* 4.0 7.1 - - - +
105A ARG* 2.6 53.5 + - + +
106A GLU* 4.4 3.6 - - - +
108A LEU* 1.3 72.4 - - - +
110A LYS* 1.3 86.0 + - + +
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Residues in contact with LYS 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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44A THR* 3.4 26.7 - - - +
45A PRO* 5.0 1.1 - - - -
106A GLU* 3.1 45.0 + - - +
107A ALA* 5.2 0.4 - - - -
108A LEU 2.6 8.3 + - - -
109A GLU* 1.3 101.7 + - - +
111A GLY* 1.3 57.9 + - - +
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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