Contacts of the helix formed by residues 120 - 127 (chain A) in PDB entry 2W9F
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 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A PHE* 3.9 1.6 - - - -
118A PRO 4.4 6.3 - - - +
119A LEU* 1.3 76.9 - - - +
121A ALA* 1.3 65.0 + - - +
122A GLU* 3.6 9.4 + - - +
123A LYS* 3.1 49.4 + - + +
124A LEU* 3.2 13.5 + - - +
44B GLU* 3.3 21.3 - - + +
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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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108A PHE* 3.3 16.4 - - + -
120A THR* 1.3 72.1 - - - +
122A GLU* 1.3 59.8 + - - +
124A LEU* 3.6 2.7 + - - +
125A CYS* 2.9 32.5 + - - -
134A PRO* 4.3 14.1 - - + -
137A LEU* 3.4 26.7 - - + -
138A LEU* 4.1 15.5 - - + -
43B GLU 4.8 2.7 - - - +
44B GLU* 3.2 14.7 + - - +
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Residues in contact with GLU 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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120A THR* 3.1 10.2 + - - +
121A ALA* 1.3 79.4 - - - +
123A LYS* 1.3 59.7 + - + +
125A CYS* 3.6 5.3 + - - +
126A ILE* 3.2 38.8 + - + +
134A PRO* 4.4 16.9 - - + +
44B GLU* 4.7 1.9 + - - +
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Residues in contact with LYS 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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71A GLN* 4.0 31.9 - - - +
119A LEU* 5.4 7.2 - - + -
120A THR* 3.1 33.9 + - + +
122A GLU* 1.3 77.3 - - - +
124A LEU* 1.3 67.2 + - - +
126A ILE* 3.3 25.1 + - + +
127A TYR* 3.1 27.4 + - + -
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A TRP* 4.4 3.5 - - + -
67A VAL* 4.5 9.0 - - + -
104A ALA* 3.5 18.6 - - + +
107A MET* 4.1 25.4 - - + -
108A PHE* 3.4 49.8 - - + -
119A LEU* 3.8 29.8 - - + -
120A THR 3.2 8.9 + - - +
121A ALA 3.8 6.7 - - - +
123A LYS* 1.3 77.6 - - - +
125A CYS* 1.3 56.1 + - - +
127A TYR* 2.9 24.5 + - - +
128A THR* 3.4 14.2 - - - +
132A ILE* 5.3 0.7 - - - -
137A LEU* 3.8 10.8 - - + -
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Residues in contact with CYS 125 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A ALA 2.9 23.0 + - - +
122A GLU 3.7 6.3 - - - +
123A LYS 3.3 0.2 - - - -
124A LEU* 1.3 78.2 - - - +
126A ILE* 1.3 59.7 + - - +
128A THR* 2.9 15.9 + - - -
130A ASN* 2.8 33.7 + - - +
132A ILE* 3.8 27.6 - - - +
133A ARG 3.7 6.5 - - - -
134A PRO* 3.4 38.1 - - + -
137A LEU* 4.7 4.3 - - - -
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Residues in contact with ILE 126 (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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122A GLU* 3.2 31.3 + - + +
123A LYS* 3.6 26.5 - - + +
124A LEU 3.2 1.4 - - - -
125A CYS* 1.3 78.2 - - - +
127A TYR* 1.3 63.5 + - + +
129A ASP* 3.2 20.1 + - - +
130A ASN* 4.0 21.7 + - - +
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Residues in contact with TYR 127 (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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63A TRP* 3.2 30.0 + - + -
66A GLU 5.5 0.2 - - - -
67A VAL* 3.9 27.1 - - + -
70A GLU* 2.9 41.3 - - + +
71A GLN* 3.1 41.0 + - + -
100A GLN* 4.6 0.7 + - - -
119A LEU* 6.0 0.7 - - + -
123A LYS* 3.1 27.1 + - + -
124A LEU* 2.9 11.5 + - + +
126A ILE* 1.3 79.5 - - + +
128A THR* 1.3 57.5 + - - +
129A ASP* 3.2 7.3 + - - -
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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