Contacts of the helix formed by residues 157 - 170 (chain F) in PDB entry 4W9E
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 THR 157 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76E TYR* 3.2 7.0 - - - -
112E CYS* 3.5 17.5 - - - +
155F VAL 3.7 1.5 + - - +
156F TYR* 1.3 76.0 - - - +
158F LEU* 1.3 65.4 + - - +
159F LYS* 3.8 4.5 + - - +
160F GLU* 3.1 26.3 + - - +
161F ARG* 3.0 21.0 + - - +
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Residues in contact with LEU 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E LYS 5.3 0.2 - - - +
73E VAL* 4.2 15.9 - - + -
76E TYR* 3.2 34.0 + - + -
93E PHE* 3.8 32.5 - - + -
95E ILE* 4.3 2.9 - - + -
103E LEU* 3.8 35.2 - - + -
107E ALA* 3.9 16.4 - - + -
112E CYS* 2.9 29.5 + - - +
157F THR* 1.3 70.1 - - - +
159F LYS* 1.3 63.5 + - - +
161F ARG* 3.2 3.7 + - + +
162F CYS* 2.9 32.8 + - - -
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Residues in contact with LYS 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E LEU* 3.7 11.6 - - + +
107E ALA* 3.5 18.9 - - + +
108E ASN* 3.2 33.7 + - - +
111E ASP* 6.0 2.5 - - - +
112E CYS 3.1 16.3 + - - +
157F THR* 3.2 4.5 - - - +
158F LEU* 1.3 76.5 - - - +
160F GLU* 1.3 63.0 + - - +
162F CYS* 3.2 6.6 + - - +
163F LEU* 3.0 33.0 + - + +
184F LEU* 4.3 5.6 - - - -
187F ASP* 3.1 35.8 + - - -
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Residues in contact with GLU 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F ASP* 5.8 0.2 - - - +
156F TYR* 4.4 11.4 - - + -
157F THR* 3.1 24.8 + - - +
159F LYS* 1.3 79.9 - - - +
161F ARG* 1.3 57.4 + - - +
163F LEU* 3.2 16.4 + - - +
164F GLN* 2.9 42.6 + - - +
167F ARG* 3.0 32.5 + - - -
192F PRO* 4.5 9.4 - - - +
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Residues in contact with ARG 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E TYR* 5.8 1.1 - - + -
92E GLU* 3.2 39.4 + - - +
93E PHE* 3.0 37.1 + - + +
94E PRO* 5.2 0.8 - - - +
95E ILE* 3.5 20.3 - - + +
82F ARG* 4.0 2.4 - - - +
156F TYR* 4.3 16.9 - - + +
157F THR 3.0 15.5 + - - +
158F LEU* 3.6 9.4 - - + +
160F GLU* 1.3 77.8 - - - +
162F CYS* 1.3 60.8 + - - +
164F GLN* 2.8 53.9 + - - +
165F VAL* 3.2 44.9 + - - +
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Residues in contact with CYS 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E ILE* 4.0 11.0 - - - -
100E ALA* 4.3 3.8 - - - +
103E LEU* 3.5 33.2 - - - -
104E LEU* 3.4 44.6 - - + +
107E ALA* 4.6 0.2 - - - -
158F LEU* 2.9 24.8 + - - -
159F LYS 3.5 7.9 - - - +
161F ARG* 1.3 75.0 - - - +
163F LEU* 1.3 62.9 + - - +
165F VAL* 3.3 3.8 + - - +
166F VAL* 3.0 29.8 + - - +
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Residues in contact with LEU 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E LEU* 3.5 21.5 - - + -
159F LYS* 3.0 31.2 + - + +
160F GLU* 3.2 25.8 + - - +
162F CYS* 1.3 75.4 - - - +
164F GLN* 1.3 58.0 + - - +
166F VAL* 3.8 0.6 - - - -
167F ARG* 2.8 60.5 + - - +
184F LEU* 4.5 2.2 - - + +
187F ASP* 4.1 21.3 - - + +
188F LEU* 3.5 39.3 - - + +
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Residues in contact with GLN 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F ARG* 2.8 15.3 + - - -
124F THR* 6.0 2.3 - - + +
126F ASP* 3.5 34.1 + - - +
156F TYR* 3.2 45.9 - - - -
160F GLU* 2.9 27.3 + - - +
161F ARG* 2.8 36.3 + - - +
163F LEU* 1.3 76.7 - - - +
165F VAL* 1.3 57.6 + - - +
167F ARG* 3.4 9.6 + - - +
168F SER* 3.0 27.9 + - - -
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Residues in contact with VAL 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E ILE* 4.1 33.2 - - + +
97E PRO* 4.7 3.6 - - + -
100E ALA* 4.0 16.6 - - + -
161F ARG* 3.2 41.7 + - - +
162F CYS* 3.3 6.5 + - - +
164F GLN* 1.3 72.3 - - - +
166F VAL* 1.3 66.4 + - - +
168F SER* 2.6 25.3 + - - +
169F LEU* 3.1 26.0 + - + +
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Residues in contact with VAL 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D MET* 5.2 2.9 - - + -
100E ALA* 4.1 22.7 - - + -
101E LEU* 4.3 20.0 - - + -
104E LEU* 4.5 10.1 - - + -
162F CYS 3.0 19.2 + - - +
165F VAL* 1.3 75.3 - - - +
167F ARG* 1.3 58.1 + - - +
169F LEU* 3.2 7.1 + - - -
170F VAL* 2.9 45.0 + - + +
175F TYR* 5.4 0.4 - - + -
178F LEU* 4.0 17.3 - - + -
188F LEU* 3.8 23.1 - - + -
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Residues in contact with ARG 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F THR* 6.4 1.8 - - + -
126F ASP* 4.6 0.6 + - - -
160F GLU* 3.0 28.7 + - - -
163F LEU* 2.8 44.9 + - - +
164F GLN* 3.5 12.1 - - - +
166F VAL* 1.3 77.0 - - - +
168F SER* 1.3 61.6 + - - +
170F VAL 3.1 17.6 - - - +
172F PRO* 5.5 1.0 - - - +
175F TYR* 3.5 23.0 + - + +
187F ASP 3.0 25.9 + - - -
188F LEU* 3.0 23.7 + - + +
190F ASP 3.6 13.5 + - - -
191F HIS* 3.7 18.8 - - - +
192F PRO* 3.7 21.8 - - - +
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Residues in contact with SER 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F THR* 6.0 7.2 - - - +
164F GLN 3.0 12.3 + - - -
165F VAL* 2.6 27.0 + - - +
167F ARG* 1.3 76.1 - - - +
169F LEU* 1.3 64.8 + - - +
170F VAL 5.3 0.2 - - - -
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Residues in contact with LEU 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D LEU* 6.3 0.7 - - + -
102D VAL 3.9 7.8 - - - +
103D MET* 3.4 46.6 - - + -
97E PRO* 3.7 35.0 - - + -
100E ALA* 4.9 0.2 - - + -
165F VAL* 3.1 28.5 + - + +
166F VAL* 3.7 3.8 - - - +
168F SER* 1.3 85.9 + - - +
170F VAL* 1.3 66.1 + - + +
171F LYS* 4.1 1.0 + - - +
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Residues in contact with VAL 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D VAL* 3.7 14.6 - - + +
103D MET* 3.4 32.8 - - + -
166F VAL* 2.9 30.0 + - + +
167F ARG 3.1 15.9 - - - +
168F SER 5.3 0.2 - - - -
169F LEU* 1.3 78.6 - - + +
171F LYS* 1.3 76.6 + - - +
172F PRO* 3.5 2.6 - - - +
174F ASN* 3.8 17.3 - - + +
175F TYR* 3.3 26.3 - - + +
178F LEU* 4.2 10.8 - - + -
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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