Contacts of the helix formed by residues 158 - 164 (chain A) in PDB entry 1I4W
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 ASN 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A TRP* 3.6 21.7 - - + -
152A SER* 3.7 2.8 + - - -
153A CYS* 2.9 27.3 + - + +
156A ASN* 3.1 44.8 + - - +
157A LYS* 1.3 78.6 - - - +
159A TRP* 1.3 75.4 + - - +
161A TYR* 2.8 20.4 + - - +
162A ARG* 4.7 1.8 - - - +
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Residues in contact with TRP 159 (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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53A LEU* 4.1 4.9 - - + -
102A PRO 4.5 2.9 - - - -
103A TYR* 5.4 2.0 - + - -
105A TRP* 3.4 30.6 - + + +
108A TYR* 2.9 58.8 - + + -
112A ILE* 6.5 0.2 - - - -
150A TRP* 3.4 62.1 - + - -
153A CYS* 3.8 24.2 - - + -
158A ASN* 1.3 80.7 - - - +
160A LEU* 1.3 94.8 + - + +
161A TYR* 3.1 16.8 + + - -
162A ARG* 3.2 26.7 + - - +
163A PHE* 4.2 2.3 - - - -
168A MET* 4.4 0.7 - - + -
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Residues in contact with LEU 160 (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 LEU* 3.8 33.7 - - + -
53A LEU* 5.0 0.9 - - + -
108A TYR* 4.1 7.0 - - + -
112A ILE* 3.9 24.0 - - + -
132A PHE* 3.9 17.6 - - + -
134A THR* 4.2 15.3 - - + +
159A TRP* 1.3 122.4 - - + +
161A TYR* 1.3 57.9 + - - +
162A ARG 3.1 1.3 - - - -
163A PHE* 3.2 27.7 + - + +
166A VAL* 4.0 9.5 - - - +
168A MET* 4.1 17.3 - - + -
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Residues in contact with TYR 161 (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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150A TRP* 2.9 37.1 + + - -
153A CYS* 3.7 32.1 - - + +
154A ILE* 3.4 34.6 - - + +
157A LYS* 3.6 18.9 - - + +
158A ASN 2.8 9.3 + - - +
159A TRP* 4.0 9.4 - + - -
160A LEU* 1.3 74.7 - - - +
162A ARG* 1.3 57.2 + - - +
163A PHE 2.9 9.8 + - - -
164A GLY* 3.3 23.7 + - - +
166A VAL* 3.5 32.1 - - + -
168A MET* 3.3 23.5 - - + +
247A MET* 4.6 5.2 + - - +
249A PRO* 4.2 14.1 - - + +
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Residues in contact with ARG 162 (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 ILE* 4.2 5.1 - - - +
113A ASP* 2.9 31.1 + - - -
122A VAL* 3.8 25.9 - - - +
157A LYS* 3.2 21.3 + - - +
158A ASN* 4.7 0.7 - - - +
159A TRP* 3.2 19.6 + - - +
160A LEU 3.1 1.8 - - - -
161A TYR* 1.3 77.9 - - - +
163A PHE* 1.3 94.6 + - + +
164A GLY 3.4 1.0 + - - -
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Residues in contact with PHE 163 (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 ILE* 3.9 23.8 - - + -
119A VAL* 5.3 2.9 - - + -
120A PRO* 3.7 45.5 - - + -
121A GLU 4.5 0.4 - - - +
122A VAL* 3.2 33.8 - - + -
123A GLN 2.9 19.5 + - - -
129A ASN* 2.9 28.8 - - - +
132A PHE* 4.2 15.7 - + + -
159A TRP 4.2 6.1 - - - -
160A LEU* 3.2 31.0 - - + +
161A TYR 2.9 1.2 - - - -
162A ARG* 1.3 118.3 - - + +
164A GLY* 1.3 56.8 + - - +
166A VAL* 4.4 0.9 - - + -
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Residues in contact with GLY 164 (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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123A GLN 3.8 15.7 - - - -
125A SER* 4.6 11.0 - - - -
129A ASN* 4.8 2.0 - - - -
161A TYR* 3.3 24.9 + - - +
162A ARG 3.4 1.6 + - - -
163A PHE* 1.3 81.5 - - - +
165A LYS* 1.3 63.2 + - - -
166A VAL* 3.1 12.2 + - - +
249A PRO* 4.7 0.2 - - - +
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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