Contacts of the helix formed by residues 112 - 123 (chain A) in PDB entry 1W45
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 LYS 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ARG* 6.2 0.2 - - - +
101A GLU 5.9 0.2 - - - +
104A ASP* 4.8 8.1 - - + +
105A ALA* 3.1 30.6 + - + +
110A GLY 5.7 0.7 - - - +
111A THR* 1.3 71.9 - - - +
113A GLU* 1.3 61.6 + - - +
114A GLY 3.3 2.9 - - - +
115A VAL* 3.2 38.6 + - + +
116A ILE* 3.5 11.1 + - - +
272A ARG* 3.9 27.5 - - - +
274A GLY* 6.1 0.2 - - - -
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Residues in contact with GLU 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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111A THR* 3.3 28.5 - - + +
112A LYS* 1.3 69.9 - - - +
114A GLY* 1.3 55.9 + - - +
116A ILE* 3.1 7.8 + - - +
117A ILE* 2.8 50.5 + - + +
151A THR* 5.1 3.4 - - + +
155A LEU* 3.8 20.6 - - + +
239A SER* 3.5 24.5 + - - -
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Residues in contact with GLY 114 (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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112A LYS* 3.3 1.2 - - - +
113A GLU* 1.3 79.7 - - - +
115A VAL* 1.3 55.4 + - - +
117A ILE* 3.9 2.9 - - - +
118A GLU* 2.9 30.8 + - - +
242A GLU* 3.7 23.9 + - - +
261A ARG* 3.6 15.0 + - - -
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Residues in contact with VAL 115 (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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101A GLU* 3.9 23.6 - - + +
102A LEU* 4.8 1.3 - - - +
105A ALA* 4.2 4.7 - - + -
112A LYS* 3.2 39.4 + - + +
113A GLU 3.2 0.8 - - - -
114A GLY* 1.3 73.2 - - - +
116A ILE* 1.3 66.6 + - - +
118A GLU* 3.4 2.5 + - - +
119A ILE* 3.1 38.5 + - + +
261A ARG* 5.7 0.4 - - - +
272A ARG* 6.1 2.2 - - - +
278A ARG* 3.9 40.4 - - - +
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Residues in contact with ILE 116 (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 LEU* 3.9 22.9 - - + -
105A ALA* 4.1 8.3 - - + -
106A MET* 4.2 17.9 - - + -
111A THR* 3.6 30.7 - - + -
112A LYS 3.5 7.8 + - - +
113A GLU* 3.1 7.9 + - - +
115A VAL* 1.3 71.6 - - - +
117A ILE* 1.3 68.2 + - - +
119A ILE* 4.1 0.2 - - - -
120A LEU* 3.0 35.1 + - + +
147A ILE* 3.6 30.3 - - + -
151A THR* 4.9 9.0 - - + -
159A LEU* 3.9 19.3 - - + -
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Residues in contact with ILE 117 (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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113A GLU* 2.8 31.9 + - + +
114A GLY* 3.9 3.8 - - - +
116A ILE* 1.3 75.6 - - + +
118A GLU* 1.3 64.6 + - - +
120A LEU* 4.2 0.4 - - - +
121A ALA* 3.1 30.3 + - + +
155A LEU* 3.9 18.4 - - + -
159A LEU* 4.2 12.6 - - + -
162A LEU* 6.6 0.4 - - - -
239A SER* 3.7 26.0 - - - +
242A GLU* 4.2 19.3 - - - +
243A ALA* 3.9 25.4 - - + +
246A THR* 3.7 27.4 - - + +
257A TYR* 5.2 0.7 - - - +
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Residues in contact with GLU 118 (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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114A GLY 2.9 19.4 + - - +
115A VAL 3.7 2.5 - - - +
116A ILE 3.3 0.4 - - - -
117A ILE* 1.3 74.8 - - - +
119A ILE* 1.3 55.7 + - - +
121A ALA* 4.3 0.7 - - - +
122A SER* 2.6 42.3 + - - +
123A ARG* 4.8 5.2 + - - +
246A THR* 4.9 0.7 - - - -
257A TYR* 3.5 32.8 + - + +
258A PHE* 5.0 0.2 - - + -
261A ARG* 2.9 33.4 + - - +
278A ARG* 2.6 41.5 + - - +
279A ASN* 3.2 27.4 + - - +
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Residues in contact with ILE 119 (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* 4.0 41.7 - - + +
101A GLU* 4.1 7.9 - - + -
102A LEU* 3.9 30.1 - - + -
115A VAL* 3.1 19.8 + - + +
116A ILE 4.2 1.1 - - - +
118A GLU* 1.3 85.9 - - - +
120A LEU* 1.3 69.5 + - + +
121A ALA 3.3 0.5 + - - -
122A SER* 3.3 4.3 + - - -
123A ARG* 3.3 42.0 + - + +
128A LEU* 5.3 2.0 - - + -
131A ILE* 5.2 4.5 - - + -
278A ARG* 3.9 21.3 - - - -
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Residues in contact with LEU 120 (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 LEU* 4.1 29.2 - - + -
116A ILE* 3.0 33.9 + - + +
117A ILE 4.2 1.1 - - - +
119A ILE* 1.3 77.8 - - - +
121A ALA* 1.3 59.1 + - - +
123A ARG 4.2 4.3 + - - +
128A LEU* 3.7 32.5 - - + +
143A LEU* 4.8 2.9 - - + -
147A ILE* 4.6 4.5 - - + -
159A LEU* 3.6 38.8 - - + +
162A LEU* 4.3 21.2 - - + +
163A LEU* 3.8 31.2 - - + -
167A ARG* 6.0 0.5 - - - -
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Residues in contact with ALA 121 (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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117A ILE* 3.1 20.1 + - + +
120A LEU* 1.3 78.7 - - - +
122A SER* 1.3 58.6 + - - +
123A ARG 3.4 1.1 + - - +
162A LEU* 4.3 12.3 - - + +
167A ARG* 3.2 24.8 + - - -
243A ALA 5.2 0.7 - - - +
246A THR* 3.6 25.4 - - + -
247A VAL* 4.1 22.5 - - + +
250A CYS* 3.9 8.9 - - - +
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Residues in contact with SER 122 (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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118A GLU 2.6 24.0 + - - -
119A ILE 3.3 0.4 + - - -
121A ALA* 1.3 77.5 - - - +
123A ARG* 1.3 90.3 + - - +
124A THR* 5.5 1.4 - - - +
127A GLN* 4.5 1.6 - - - +
167A ARG* 4.2 5.0 + - - +
250A CYS* 3.9 18.4 - - - -
254A LEU* 4.0 21.0 - - - +
257A TYR* 4.4 1.6 - - - -
258A PHE* 3.7 26.9 - - - -
283A ARG* 5.0 2.6 + - - -
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Residues in contact with ARG 123 (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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10A GLN* 5.3 1.4 + - - -
98A GLU* 2.9 39.5 + - - +
118A GLU* 4.3 5.7 + - - -
119A ILE* 3.3 35.2 + - + +
120A LEU 4.2 4.0 + - - +
121A ALA 3.4 0.9 - - - +
122A SER* 1.3 111.6 + - - +
124A THR* 1.3 66.5 + - - +
127A GLN* 3.3 29.7 + - + +
128A LEU* 4.0 21.7 - - + +
131A ILE* 5.0 7.9 - - + -
167A ARG* 4.0 17.5 + - - +
258A PHE* 4.1 14.3 - - - -
278A ARG* 5.5 2.8 - - - +
279A ASN* 5.5 0.2 + - - -
282A SER* 3.3 24.4 + - - -
283A ARG* 4.4 16.1 - - - +
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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