Contacts of the helix formed by residues 145 - 156 (chain A) in PDB entry 4WUR
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 SER 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A MET* 3.5 23.7 - - - +
102A ARG* 3.1 23.0 + - - -
140A HIS* 2.6 37.6 + - - +
144A ASP* 1.3 72.8 + - - +
146A THR* 1.3 59.1 + - - +
147A ASP 3.4 2.5 - - - -
148A PHE* 3.3 2.9 + - - +
149A ILE* 2.8 34.7 + - - +
401A IPA 3.6 11.3 - - - +
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Residues in contact with THR 146 (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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87A LYS* 4.0 27.8 - - + +
90A VAL* 4.0 19.2 - - + +
91A HIS* 4.5 17.9 - - + -
144A ASP* 3.6 14.5 + - - -
145A SER* 1.3 72.8 - - - +
147A ASP* 1.3 71.9 + - - +
149A ILE* 3.7 1.4 - - - +
150A ALA* 2.9 24.1 + - - +
401A IPA 3.5 25.7 + - - +
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Residues in contact with ASP 147 (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 PHE* 4.0 8.8 - - + -
87A LYS* 2.6 37.6 + - - -
136A ALA* 3.7 21.4 - - + +
139A LYS* 3.0 36.7 + - + +
144A ASP* 4.8 3.0 + - - +
145A SER 3.4 0.4 - - - -
146A THR* 1.3 77.8 - - - +
148A PHE* 1.3 65.4 + - - +
151A LEU* 2.8 29.0 + - + +
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Residues in contact with PHE 148 (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* 4.9 9.6 - - + -
120A LEU* 3.8 23.8 - - + -
128A PHE* 4.0 12.1 - + - -
133A LEU* 3.7 28.5 - - + -
136A ALA* 3.4 19.6 + - + +
137A PHE* 3.5 47.3 - + + -
140A HIS* 3.7 29.2 - + + -
145A SER 3.3 4.6 + - - +
146A THR 3.2 0.4 - - - -
147A ASP* 1.3 81.4 - - - +
149A ILE* 1.3 58.4 + - + +
151A LEU* 3.6 1.6 - - - +
152A ILE* 2.9 65.6 + - + +
173A VAL* 4.6 0.2 - - + -
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Residues in contact with ILE 149 (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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90A VAL* 4.1 4.5 - - + -
93A TRP* 3.6 18.2 - - + -
95A MET* 3.5 30.5 - - + -
104A LEU* 4.3 13.9 - - + -
113A LEU* 4.4 9.5 - - + +
117A ILE* 4.7 16.4 - - + -
145A SER* 2.8 27.1 + - - +
146A THR* 3.7 3.8 - - - +
148A PHE* 1.3 75.5 - - + +
150A ALA* 1.3 61.8 + - - +
152A ILE* 3.3 8.3 + - - +
153A MET* 3.1 42.8 + - + +
401A IPA 3.6 18.2 - - + -
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Residues in contact with ALA 150 (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 PHE* 3.9 8.2 - - + +
86A LEU* 3.5 12.9 - - - +
87A LYS* 3.6 44.4 - - + +
90A VAL* 4.9 1.8 - - + -
146A THR 2.9 18.7 + - - +
149A ILE* 1.3 70.7 - - - +
151A LEU* 1.3 67.6 + - - +
153A MET* 3.4 12.9 + - + -
154A ALA* 2.9 20.3 + - - +
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Residues in contact with LEU 151 (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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72A TYR* 4.1 10.5 - - + -
79A PHE* 3.6 19.5 - - + -
83A PHE* 3.3 28.3 - - + -
132A ALA* 3.6 23.1 - - + +
133A LEU* 4.1 13.0 - - + -
136A ALA* 3.5 28.7 - - + -
147A ASP* 2.8 14.7 + - + +
148A PHE 3.6 3.8 - - - +
150A ALA* 1.3 78.6 - - - +
152A ILE* 1.3 56.5 + - - +
154A ALA* 3.1 2.8 + - - +
155A TYR* 2.9 62.5 + - + -
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Residues in contact with ILE 152 (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 LEU* 4.4 7.9 - - + -
116A VAL* 4.7 7.0 - - + -
117A ILE* 4.9 7.6 - - + -
120A LEU* 4.2 11.0 - - + -
133A LEU* 4.7 4.9 - - + -
148A PHE* 2.9 64.9 + - + +
149A ILE* 3.7 7.0 - - - +
151A LEU* 1.3 76.8 - - - +
153A MET* 1.3 58.1 + - - +
155A TYR* 3.5 7.6 + - - +
156A GLY* 2.8 26.0 + - - -
169A LEU* 3.6 27.9 - - + +
173A VAL* 3.8 22.8 - - + +
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Residues in contact with MET 153 (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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86A LEU* 3.6 30.3 - - + -
90A VAL* 3.5 29.2 - - + -
93A TRP* 3.8 7.6 - - - -
112A TYR* 4.1 6.3 - - - -
113A LEU* 3.6 33.4 - - + -
149A ILE* 3.1 29.5 + - + +
150A ALA* 3.7 9.9 - - - -
152A ILE* 1.3 75.2 - - - +
154A ALA* 1.3 59.5 + - - +
156A GLY 3.1 0.2 + - - -
157A ASN 2.7 25.1 + - - -
158A CYS* 2.8 32.7 + - + +
160A PHE* 5.2 6.7 - - - -
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Residues in contact with ALA 154 (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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79A PHE* 3.6 23.7 - - + -
82A ARG* 2.9 34.1 + - - +
83A PHE* 3.9 21.5 - - + +
86A LEU* 3.3 13.4 - - + +
150A ALA 2.9 14.2 + - - +
151A LEU 3.1 8.5 + - - +
153A MET* 1.3 75.0 - - - +
155A TYR* 1.3 63.9 + - - +
157A ASN* 3.1 5.7 + - - +
158A CYS 5.3 0.2 - - - -
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Residues in contact with TYR 155 (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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72A TYR* 2.6 40.2 + + - +
74A PRO 5.9 0.2 - - - -
75A VAL* 4.1 9.0 - - + -
79A PHE* 3.7 20.9 - + - -
130A ILE* 3.3 24.1 - - + +
133A LEU* 4.3 30.3 - - + -
151A LEU* 2.9 45.8 + - + +
152A ILE* 3.9 6.5 - - - +
154A ALA* 1.3 77.6 - - - +
156A GLY* 1.3 58.4 + - - +
157A ASN* 3.2 6.1 + - - +
169A LEU* 6.1 0.2 - - + -
172A THR* 5.0 7.0 + - - +
173A VAL* 6.1 3.6 - - + -
176A LYS* 4.0 24.1 - - + -
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Residues in contact with GLY 156 (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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152A ILE 2.8 18.1 + - - -
153A MET 3.6 0.4 - - - -
155A TYR* 1.3 75.0 - - - +
157A ASN* 1.3 72.2 + - - +
158A CYS* 3.0 6.5 + - - -
168A ARG* 2.9 28.5 + - - -
169A LEU* 3.6 20.6 - - - +
172A THR* 4.5 5.2 - - - -
72B ARG* 3.9 1.2 + - - -
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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