Contacts of the helix formed by residues 102 - 113 (chain Z) in PDB entry 2W4V
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 102 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93Z PHE* 4.7 0.8 - - - -
100Z PHE* 4.6 7.2 - - - -
101Z ILE* 1.3 80.5 - - - +
103Z GLY* 1.3 68.4 + - - +
104Z ALA* 3.8 7.4 + - - +
105Z GLU* 2.9 32.9 + - - +
106Z LEU* 3.1 20.4 + - - +
136Z GLU 5.8 0.9 - - - -
137Z GLY 3.5 13.9 - - - -
138Z ASN* 4.0 2.5 - - - +
139Z VAL* 4.5 1.8 - - - -
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Residues in contact with GLY 103 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102Z SER* 1.3 71.6 - - - +
104Z ALA* 1.3 66.5 + - - +
106Z LEU* 2.8 20.2 + - - +
107Z ARG* 2.8 14.7 + - - +
133Z GLU* 5.9 3.6 - - - -
137Z GLY 3.2 13.4 + - - -
138Z ASN* 4.7 0.8 - - - +
139Z VAL* 4.7 12.2 - - - +
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Residues in contact with ALA 104 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102Z SER* 4.0 7.4 - - - +
103Z GLY* 1.3 72.9 - - - +
105Z GLU* 1.3 66.5 + - + +
107Z ARG* 3.3 31.3 + - - +
108Z HIS* 3.1 18.4 + - - +
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Residues in contact with GLU 105 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93Z PHE* 2.4 55.5 - - + -
102Z SER* 2.9 21.7 + - - +
103Z GLY 3.0 0.2 + - - -
104Z ALA* 1.3 76.6 - - + +
106Z LEU* 1.3 68.3 + - - +
107Z ARG 3.1 1.3 - - - -
108Z HIS* 2.7 28.3 + - - +
109Z VAL* 2.9 17.1 + - - +
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Residues in contact with LEU 106 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90Z PHE* 3.4 13.5 - - + -
101Z ILE* 3.0 38.8 - - + +
102Z SER 3.1 4.6 + - - +
103Z GLY* 2.8 10.2 + - - +
105Z GLU* 1.3 78.0 - - - +
107Z ARG* 1.3 61.9 + - - +
109Z VAL* 2.2 43.2 - - + +
110Z LEU* 3.1 8.4 + - + +
131Z LEU* 5.4 9.6 - - + -
139Z VAL* 3.2 31.2 - - + -
141Z TYR* 3.7 21.3 - - + -
144Z PHE* 5.5 3.4 - - + -
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Residues in contact with ARG 107 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Z GLY 2.8 11.3 + - - +
104Z ALA* 3.3 32.8 + - - +
106Z LEU* 1.3 79.1 - - - +
108Z HIS* 1.3 62.9 + - - +
110Z LEU* 3.7 3.9 - - - +
111Z THR* 2.9 57.6 + - + +
122Z VAL* 4.6 18.6 - - + -
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Residues in contact with HIS 108 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93Z PHE* 6.2 2.9 - + + -
104Z ALA 3.1 9.6 + - - +
105Z GLU* 2.7 29.6 + - - +
107Z ARG* 1.3 81.8 - - - +
109Z VAL* 1.3 62.3 + - + -
111Z THR* 3.7 6.7 - - - -
112Z ALA* 2.7 54.5 + - + +
113Z LEU* 4.8 13.3 - - + +
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Residues in contact with VAL 109 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782C ILE* 4.2 14.2 - - + +
90Z PHE* 6.3 0.9 - - + -
93Z PHE* 4.8 20.0 - - + -
101Z ILE* 4.8 3.1 - - + -
105Z GLU 2.9 17.9 + - - +
106Z LEU* 2.2 54.5 - - + +
108Z HIS* 1.3 84.3 - - + +
110Z LEU* 1.3 73.6 + - + +
113Z LEU* 3.2 36.6 + - + +
141Z TYR* 6.1 0.9 - - + -
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Residues in contact with LEU 110 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782C ILE* 5.5 4.7 - - + +
785C PHE* 4.5 20.9 - - + -
786C GLN* 4.2 24.1 - - + +
789C ILE* 4.8 9.4 - - + -
106Z LEU 3.1 9.8 + - - +
107Z ARG* 3.7 8.7 - - - +
109Z VAL* 1.3 91.3 - - + +
111Z THR* 1.3 57.5 + - + +
113Z LEU 3.8 2.9 - - - +
116Z ARG* 3.8 5.0 - - - -
117Z LEU* 2.4 40.4 + - + +
122Z VAL* 5.0 5.4 - - + -
125Z ILE* 4.4 25.1 - - + -
126Z ILE* 6.3 0.2 - - + -
144Z PHE* 4.9 14.4 - - + -
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Residues in contact with THR 111 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Z ARG* 2.9 46.7 + - + +
108Z HIS* 3.6 6.8 + - - -
110Z LEU* 1.3 68.9 - - + +
112Z ALA* 1.3 61.9 + - - +
116Z ARG* 3.1 42.0 + - - +
117Z LEU* 2.4 40.8 - - + +
118Z SER 4.5 0.2 - - - +
119Z ASP* 4.6 7.9 - - + -
122Z VAL* 4.3 10.8 - - + -
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Residues in contact with ALA 112 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Z HIS* 2.7 47.0 + - + +
111Z THR* 1.3 78.1 + - - +
113Z LEU* 1.3 63.4 + - - +
114Z GLY 4.4 0.5 - - - +
116Z ARG* 3.6 24.8 + - - +
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Residues in contact with LEU 113 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782C ILE* 4.4 20.5 - - + +
786C GLN* 5.9 1.0 - - - +
108Z HIS* 3.5 14.3 + - + +
109Z VAL* 3.2 30.4 + - + +
110Z LEU 3.8 8.8 - - - +
112Z ALA* 1.3 82.2 - - - +
114Z GLY* 1.3 76.2 + - - +
115Z GLU 4.2 0.7 - - - +
116Z ARG 3.9 1.6 + - - -
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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