Contacts of the helix formed by residues 96 - 109 (chain A) in PDB entry 4I93
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 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A TRP 3.3 3.7 - - - +
95A PRO* 1.3 78.2 - - + +
97A SER* 1.3 63.5 + - - +
98A ARG* 2.9 25.0 + - - +
99A GLN* 3.2 39.9 + - + +
100A PHE* 3.1 21.0 + - - +
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Residues in contact with SER 97 (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 PRO 3.5 2.7 + - - -
96A ASP* 1.3 70.8 + - - +
98A ARG* 1.3 60.5 + - - +
100A PHE* 3.6 3.5 - - - +
101A LEU* 2.9 33.2 + - - +
123A TYR* 4.1 26.2 + - - -
128A ARG* 2.8 35.1 + - - +
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Residues in contact with ARG 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 ASP* 2.9 11.7 + - - +
97A SER* 1.3 79.5 - - - +
99A GLN* 1.3 59.2 + - + +
101A LEU* 3.3 25.6 + - - +
102A GLU* 2.6 73.5 + - + +
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Residues in contact with GLN 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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94A TRP* 4.4 8.1 - - + -
95A PRO* 5.1 4.2 - - - +
96A ASP* 3.2 43.2 + - + +
98A ARG* 1.3 78.5 - - + +
100A PHE* 1.3 65.6 + - - +
102A GLU* 3.4 6.1 + - - +
103A GLU* 3.1 26.9 + - - +
207A ARG* 3.1 63.5 + - - +
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Residues in contact with PHE 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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89A PHE* 4.1 13.0 - + - -
94A TRP* 3.8 33.2 - + + -
96A ASP 3.1 14.0 + - - +
97A SER 3.6 5.8 - - - +
99A GLN* 1.3 78.8 - - - +
101A LEU* 1.3 61.3 + - - +
103A GLU* 3.3 3.5 + - - +
104A ALA* 2.9 27.2 + - - +
121A CYS* 4.1 12.3 - - + -
122A CYS 3.8 12.3 - - - -
123A TYR* 4.3 10.1 - - + -
128A ARG* 3.7 30.1 - - + -
129A LEU 3.6 36.6 - - - -
130A LEU* 3.8 12.8 - - + -
203A MSE 3.6 23.6 - - + -
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Residues in contact with LEU 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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41A PHE* 4.5 3.8 - - + -
43A GLU* 3.7 24.7 - - + +
97A SER 2.9 20.7 + - - +
98A ARG* 3.7 31.2 - - - +
100A PHE* 1.3 78.5 - - - +
102A GLU* 1.3 59.9 + - - +
104A ALA* 3.3 2.4 + - - +
105A LYS* 2.8 57.9 + - + +
121A CYS* 3.7 24.7 - - - -
123A TYR* 3.9 22.4 - - + +
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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 ARG* 2.6 58.4 + - + +
99A GLN* 3.4 5.6 + - - +
100A PHE 3.3 0.2 - - - -
101A LEU* 1.3 76.1 - - - +
103A GLU* 1.3 61.5 + - - +
105A LYS* 3.5 29.9 + - - +
106A ALA* 3.0 23.7 + - - +
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Residues in contact with GLU 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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94A TRP* 4.0 23.2 - - + -
99A GLN 3.1 15.5 + - - +
100A PHE 3.7 6.7 - - - +
102A GLU* 1.3 74.5 - - - +
104A ALA* 1.3 64.7 + - - +
106A ALA* 3.1 5.5 + - - +
107A VAL* 3.0 25.1 + - - +
176A ARG* 2.8 43.7 + - - -
202A LEU 4.5 0.5 - - - +
203A MSE 3.8 25.3 - - + +
204A LYS* 5.3 3.5 + - - -
207A ARG* 4.4 10.3 - - - +
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Residues in contact with ALA 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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41A PHE* 3.4 18.1 - - + -
100A PHE* 2.9 19.8 + - + +
101A LEU 3.7 3.1 - - - +
103A GLU* 1.3 77.7 - - - +
105A LYS* 1.3 57.4 + - - +
107A VAL 3.2 1.2 + - - -
108A GLY 2.8 25.5 + - - -
118A LEU* 3.3 11.5 - - - +
121A CYS* 3.9 11.2 - - + -
130A LEU* 3.7 25.6 - - + -
203A MSE 3.7 9.4 - - - -
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Residues in contact with LYS 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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41A PHE* 3.5 33.0 - - + +
98A ARG* 5.6 0.2 - - - +
101A LEU* 2.8 39.2 + - + +
102A GLU* 3.7 31.4 - - - +
104A ALA* 1.3 72.2 - - - +
106A ALA* 1.3 63.3 - - - +
108A GLY* 3.1 10.2 + - - -
109A GLN* 3.2 22.8 + - - +
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Residues in contact with ALA 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 3.0 14.7 + - - +
103A GLU* 3.1 10.1 + - - +
105A LYS* 1.3 75.5 - - - +
107A VAL* 1.3 65.1 + - - +
109A GLN* 3.2 24.2 + - - +
110A LEU* 3.6 9.2 - - - +
176A ARG* 3.6 24.4 - - - +
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Residues in contact with VAL 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 GLU 3.0 13.3 + - - +
104A ALA* 3.7 7.0 - - - +
106A ALA* 1.3 76.3 - - - +
108A GLY* 1.3 56.8 + - - +
109A GLN 3.1 0.2 - - - -
110A LEU* 3.1 31.5 + - - +
118A LEU* 3.7 26.3 + - + +
130A LEU* 6.3 1.3 - - + -
176A ARG* 3.8 31.6 - - - +
199A CYS* 4.2 14.4 - - + +
202A LEU* 4.0 27.6 - - + -
203A MSE 3.9 16.2 - - + -
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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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41A PHE* 3.7 28.2 + - - +
104A ALA 2.8 15.6 + - - -
105A LYS 3.1 6.9 + - - -
107A VAL* 1.3 76.3 - - - +
109A GLN* 1.3 61.1 + - - +
110A LEU 3.2 0.4 - - - -
111A ARG* 3.3 25.0 + - - +
118A LEU* 3.7 12.1 - - - +
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Residues in contact with GLN 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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41A PHE* 5.7 2.9 - - - +
105A LYS* 3.2 17.1 + - - +
106A ALA* 3.4 13.9 - - - +
107A VAL 3.1 1.2 - - - -
108A GLY* 1.3 76.9 - - - +
110A LEU* 1.3 68.4 + - + +
111A ARG* 3.6 8.8 + - - +
170A TYR* 4.5 1.7 + - - -
174A LYS* 5.9 1.4 - - - +
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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