Contacts of the helix formed by residues 116 - 128 (chain D) in PDB entry 2ZTC
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 GLY 116 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110D THR* 4.6 2.9 - - - -
114D GLY 3.6 5.7 + - - -
115D ILE* 1.3 77.2 - - - +
117D LYS* 1.3 67.9 + - - -
118D ARG 3.3 2.7 - - - -
119D GLY* 3.1 9.2 + - - -
120D ALA* 2.9 19.8 + - - +
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Residues in contact with LYS 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D VAL* 4.8 5.3 - - + +
110D THR* 4.2 17.3 + - + +
116D GLY* 1.3 72.2 - - - +
118D ARG* 1.3 66.1 + - - +
120D ALA* 3.2 10.2 + - - +
121D GLU* 3.4 19.2 + - - +
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Residues in contact with ARG 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D GLY 3.3 0.4 - - - -
117D LYS* 1.3 76.4 - - - +
119D GLY* 1.3 65.3 + - - +
121D GLU* 3.2 25.8 + - - +
122D ARG* 3.3 25.6 + - + +
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Residues in contact with GLY 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D ILE* 4.4 4.9 - - - -
116D GLY* 3.1 15.6 + - - -
118D ARG* 1.3 77.7 - - - +
120D ALA* 1.3 62.0 + - - +
122D ARG* 3.2 33.6 + - - +
123D MET* 3.3 20.2 + - - +
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Residues in contact with ALA 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D VAL* 3.7 25.4 - - + +
109D LEU* 3.7 28.8 - - + +
110D THR* 4.1 4.0 - - - +
115D ILE* 3.8 11.0 - - + +
116D GLY 2.9 13.9 + - - +
117D LYS 3.2 8.5 + - - +
119D GLY* 1.3 71.8 - - - +
121D GLU* 1.3 64.2 + - - +
123D MET* 3.3 7.0 + - - +
124D VAL* 3.1 25.5 + - - +
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Residues in contact with GLU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D VAL* 4.3 20.7 - - + +
117D LYS* 3.4 18.4 + - - +
118D ARG* 3.2 16.0 + - - +
120D ALA* 1.3 80.2 - - - +
122D ARG* 1.3 66.0 + - + +
123D MET 3.0 0.3 + - - -
124D VAL* 3.2 4.3 + - - +
125D LEU* 2.9 23.9 + - - +
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Residues in contact with ARG 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D VAL* 5.0 5.8 - - + +
78D SER* 3.5 24.0 + - - -
79D GLY* 5.2 3.6 - - - -
118D ARG* 3.3 22.4 + - + +
119D GLY* 3.2 20.3 + - - +
121D GLU* 1.3 76.5 - - + +
123D MET* 1.3 53.1 + - + +
125D LEU* 3.2 7.7 - - - +
126D GLU* 2.8 54.8 + - - +
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Residues in contact with MET 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D LEU* 4.6 21.3 - - + -
77D VAL* 3.9 28.7 - - + -
80D VAL* 4.2 19.7 - - + -
84D LEU* 5.4 3.1 - - + -
88D ALA* 5.9 3.4 - - + -
97D LEU* 6.1 0.7 - - + -
101D LEU* 4.6 9.9 - - + -
109D LEU* 4.6 15.5 - - + -
115D ILE* 4.2 29.2 - - + -
119D GLY 3.3 19.3 - - - +
120D ALA* 3.5 9.4 - - - +
122D ARG* 1.3 72.9 - - + +
124D VAL* 1.3 67.7 + - - +
126D GLU* 2.9 17.4 + - - +
127D LEU* 3.0 21.0 + - + +
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Residues in contact with VAL 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU* 4.0 21.3 - - - +
104D GLY* 3.9 31.6 - - - +
106D VAL* 4.6 5.8 - - + -
109D LEU* 3.7 26.7 - - + -
120D ALA 3.1 5.8 + - - +
121D GLU* 3.7 8.5 - - - +
123D MET* 1.3 77.4 - - - +
125D LEU* 1.3 63.6 + - - +
128D ARG* 2.9 54.6 + - - +
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Residues in contact with LEU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D GLU 2.9 13.3 + - - +
122D ARG* 3.2 11.4 - - - +
124D VAL* 1.3 81.1 - - - +
126D GLU* 1.3 73.2 + - - +
127D LEU 2.8 7.8 + - - -
128D ARG* 3.7 17.4 + - - +
129D ASP 5.0 1.2 + - - -
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Residues in contact with GLU 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D SER* 5.7 3.1 - - - +
77D VAL* 4.0 38.5 - - + +
78D SER 4.8 2.9 + - - -
122D ARG* 2.8 39.0 + - - +
123D MET 2.9 4.4 + - - +
125D LEU* 1.3 88.3 - - - +
127D LEU* 1.3 60.4 + - + +
130D LYS* 3.6 17.7 - - - +
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Residues in contact with LEU 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D LEU* 6.0 0.7 - - + -
73D THR* 3.8 26.7 - - + +
74D LEU* 4.7 11.7 - - + -
76D SER* 5.1 1.1 - - - +
77D VAL* 3.9 26.0 - - + -
101D LEU* 3.0 47.1 - - + +
123D MET* 3.0 16.3 + - + +
124D VAL 3.8 0.2 - - - -
125D LEU 2.8 6.3 + - - -
126D GLU* 1.3 78.2 - - + +
128D ARG* 1.3 63.2 + - - +
129D ASP 3.3 2.0 - - - +
130D LYS* 3.4 23.4 + - + -
131D VAL* 3.3 19.1 - - + +
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Residues in contact with ARG 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU 3.7 18.6 - - - +
102D ALA* 3.5 35.8 - - + +
103D ASP 5.1 1.4 + - - -
104D GLY* 4.2 8.9 - - - -
124D VAL* 2.9 37.9 + - - +
125D LEU* 3.7 16.2 + - - +
127D LEU* 1.3 77.8 - - - +
129D ASP* 1.3 59.0 + - + +
130D LYS 3.3 3.6 + - - -
131D VAL* 4.2 7.1 + - - +
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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