Contacts of the helix formed by residues 118 - 130 (chain Z) in PDB entry 2W4T
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 118 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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790C ARG* 4.8 2.8 - - - +
117Z LEU* 1.3 99.7 - - - +
119Z ASP* 1.3 62.1 + - - +
120Z GLU* 3.5 9.2 + - - +
121Z ASP* 2.3 41.0 + - - -
122Z VAL* 2.8 5.0 + - - +
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Residues in contact with ASP 119 (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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111Z THR* 4.6 8.2 - - + +
117Z LEU 4.4 0.2 - - - -
118Z SER* 1.3 73.4 - - - +
120Z GLU* 1.3 67.4 + - - +
122Z VAL* 2.3 32.9 - - + +
123Z ASP* 2.7 18.0 + - - +
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Residues in contact with GLU 120 (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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118Z SER* 3.1 8.7 - - - +
119Z ASP* 1.3 92.6 - - - +
121Z ASP* 1.3 56.6 + - - +
122Z VAL 3.0 0.2 - - - -
123Z ASP* 2.3 37.4 - - - +
124Z GLU* 2.3 35.6 + - + +
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Residues in contact with ASP 121 (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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786C GLN* 6.1 0.4 - - - -
789C ILE* 4.4 16.4 - - + -
790C ARG* 5.0 11.6 + - - -
793C LEU* 3.0 27.1 - - + +
117Z LEU* 4.3 8.5 - - + -
118Z SER* 2.3 34.4 + - - +
120Z GLU* 1.3 77.0 - - - +
122Z VAL* 1.3 50.4 + - - +
124Z GLU* 3.0 13.4 - - - +
125Z ILE* 2.6 38.5 - - - +
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Residues in contact with VAL 122 (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* 4.6 24.0 - - + -
110Z LEU* 5.0 5.8 - - + -
111Z THR* 4.3 7.2 - - + -
117Z LEU* 3.4 14.9 - - + +
118Z SER 2.8 10.3 + - - +
119Z ASP* 2.3 49.8 - - + +
121Z ASP* 1.3 69.5 - - - +
123Z ASP* 1.3 59.4 + - + +
124Z GLU 2.8 3.8 - - - -
125Z ILE* 2.5 20.2 - - + +
126Z ILE* 2.5 36.9 + - + +
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Residues in contact with ASP 123 (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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119Z ASP 2.7 7.1 - - - +
120Z GLU* 2.3 51.6 - - - +
122Z VAL* 1.3 79.7 - - + +
124Z GLU* 1.3 78.8 + - - +
126Z ILE* 2.3 44.0 - - + +
127Z LYS* 3.1 8.8 + - - +
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Residues in contact with GLU 124 (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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792C TYR* 3.9 4.9 - - - +
793C LEU* 4.9 13.4 - - + +
120Z GLU* 2.3 40.8 + - + +
121Z ASP* 3.0 16.2 - - - +
122Z VAL 2.8 0.6 - - - -
123Z ASP* 1.3 88.3 - - - +
125Z ILE* 1.3 58.4 + - + +
126Z ILE 3.0 2.7 - - - -
127Z LYS* 2.8 30.1 + - - +
128Z LEU* 2.8 15.6 + - + +
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Residues in contact with ILE 125 (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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789C ILE* 4.2 22.9 - - + +
792C TYR* 2.8 43.7 + - + +
793C LEU* 5.1 1.1 - - + -
110Z LEU* 4.4 13.9 - - + -
121Z ASP* 2.6 29.4 + - + +
122Z VAL* 2.5 37.9 - - + +
124Z GLU* 1.3 69.4 - - + +
126Z ILE* 1.3 63.0 + - + +
128Z LEU* 3.7 1.8 - - - -
129Z THR* 2.7 38.5 + - + +
144Z PHE* 4.2 21.8 - - + -
148Z VAL* 5.8 1.1 - - + -
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Residues in contact with ILE 126 (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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110Z LEU* 6.3 0.2 - - + -
122Z VAL* 2.5 41.5 - - + +
123Z ASP* 2.3 52.5 - - + +
124Z GLU 2.8 0.2 + - - -
125Z ILE* 1.3 83.8 - - + +
127Z LYS* 1.3 61.8 + - + +
129Z THR* 3.1 2.9 + - - -
130Z ASP 2.8 29.6 + - - -
131Z LEU* 3.1 25.6 + - + +
144Z PHE* 5.2 3.8 - - + -
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Residues in contact with LYS 127 (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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123Z ASP 3.4 9.6 - - - +
124Z GLU* 2.8 12.4 + - - +
126Z ILE* 1.3 79.8 - - + +
128Z LEU* 1.3 71.2 + - + +
130Z ASP* 2.8 24.5 + - - +
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Residues in contact with LEU 128 (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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792C TYR* 2.6 43.1 - - + +
793C LEU* 5.1 2.5 - - + -
796C LYS* 2.3 71.1 + - + +
124Z GLU* 2.8 15.6 + - + +
125Z ILE 3.7 2.9 - - - +
127Z LYS* 1.3 72.5 - - + +
129Z THR* 1.3 55.2 + - + +
130Z ASP* 2.7 28.4 + - - +
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Residues in contact with THR 129 (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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792C TYR* 4.3 19.7 - - + -
125Z ILE 2.7 20.8 + - - +
126Z ILE 3.1 5.2 + - - -
128Z LEU* 1.3 70.7 - - + +
130Z ASP* 1.3 65.0 + - - +
131Z LEU* 3.2 17.2 + - - +
144Z PHE* 3.9 3.9 - - + -
147Z LYS* 2.8 56.5 + - + +
148Z VAL* 4.5 16.4 - - + +
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Residues in contact with ASP 130 (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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126Z ILE 2.8 9.6 + - - -
127Z LYS* 2.8 18.4 - - - +
128Z LEU 2.7 21.5 + - - +
129Z THR* 1.3 79.9 - - - +
131Z LEU* 1.3 62.6 + - - +
132Z GLN* 3.6 5.4 + - - +
147Z LYS* 4.0 7.6 + - - +
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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