Contacts of the helix formed by residues 110 - 122 (chain D) in PDB entry 3CB4
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 ALA 110 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D GLU* 1.3 71.7 - - - +
111D GLN* 1.3 62.9 + - - +
112D THR 3.3 0.4 - - - -
113D LEU* 3.1 25.1 + - + +
114D ALA* 3.3 15.1 + - - +
407D HIS* 4.7 3.6 - - + +
409D LEU* 4.3 16.9 - - + +
467D SER* 3.0 39.1 + - - +
468D LEU 4.9 0.7 - - - -
469D ASP* 4.4 17.4 - - + +
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Residues in contact with GLN 111 (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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12D HIS* 3.1 40.7 + - + -
80D GLY* 3.3 29.2 - - - +
81D HIS* 5.6 3.8 - - - +
109D GLU* 3.1 27.5 + - - +
110D ALA* 1.3 74.0 + - - +
112D THR* 1.3 65.3 + - + +
113D LEU 3.1 1.3 + - - -
114D ALA* 3.8 7.3 + - - +
115D ASN* 3.9 20.1 + - - +
467D SER* 4.4 9.3 - - - -
468D LEU 5.5 4.1 + - - +
469D ASP* 4.8 8.7 - - - +
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Residues in contact with THR 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ILE* 4.0 20.5 - - + +
11D ALA* 3.4 35.2 - - - +
12D HIS* 4.1 13.2 - - + -
80D GLY* 6.1 0.4 - - - -
100D LEU* 4.2 12.6 - - - +
101D VAL 5.9 0.2 - - - +
108D VAL* 3.3 20.3 - - - +
109D GLU* 3.0 20.0 + - + +
111D GLN* 1.3 81.5 - - + +
113D LEU* 1.3 57.4 + - - +
115D ASN 4.4 0.4 - - - -
116D CYS* 3.1 24.5 + - - +
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Residues in contact with LEU 113 (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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108D VAL* 3.5 25.4 - - + -
109D GLU* 3.8 9.9 - - - +
110D ALA* 3.1 27.6 + - - +
111D GLN 3.1 0.6 - - - -
112D THR* 1.3 78.1 - - - +
114D ALA* 1.3 56.8 + - - +
115D ASN 3.2 2.0 - - - -
116D CYS* 2.8 4.3 + - + +
117D TYR* 2.7 67.2 + - + +
150D ILE* 3.9 17.0 - - + -
151D VAL* 3.6 23.8 - - + -
409D LEU* 3.8 24.9 - - + -
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Residues in contact with ALA 114 (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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82D VAL* 4.0 13.5 - - + -
110D ALA 3.3 4.5 + - - +
111D GLN 3.8 2.9 + - - +
113D LEU* 1.3 77.5 - - - +
115D ASN* 1.3 58.1 + - - +
117D TYR* 3.6 10.9 + - - +
118D THR* 2.7 36.9 + - - +
469D ASP* 3.3 39.3 - - - +
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Residues in contact with ASN 115 (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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10D ILE* 3.9 26.5 - - + +
78D THR* 3.6 15.3 - - + +
79D PRO 3.4 10.1 + - - -
80D GLY* 3.3 30.7 - - - -
81D HIS 4.8 7.3 + - - -
82D VAL* 5.2 2.6 - - - +
88D VAL* 3.9 21.6 - - + +
92D LEU* 4.1 4.6 - - + +
111D GLN 3.9 11.8 + - - +
112D THR 4.7 0.2 - - - +
113D LEU 3.2 0.2 - - - -
114D ALA* 1.3 82.9 - - - +
116D CYS* 1.3 57.5 + - - +
118D THR* 3.3 8.1 + - - -
119D ALA* 3.0 28.1 + - - +
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Residues in contact with CYS 116 (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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10D ILE* 4.3 7.6 - - + -
100D LEU* 3.8 25.8 - - - -
112D THR 3.1 18.9 + - - +
113D LEU* 2.8 10.6 + - + +
115D ASN* 1.3 78.7 - - - +
117D TYR* 1.3 65.5 + - + +
119D ALA* 3.4 5.8 - - - +
120D MET* 3.2 30.2 + - - +
126D VAL* 4.3 16.4 - - - -
151D VAL* 3.6 30.1 - - + -
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Residues in contact with TYR 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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113D LEU* 2.7 57.4 + - + +
114D ALA* 4.1 9.0 - - - +
116D CYS* 1.3 70.2 - - - +
118D THR* 1.3 60.8 + - + +
120D MET* 3.1 22.1 + - + +
121D GLU* 2.9 40.3 + - - +
150D ILE* 3.6 30.8 + - - +
151D VAL* 4.3 13.7 - - + -
407D HIS* 6.1 9.6 - + + -
409D LEU* 5.6 1.6 - - - +
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Residues in contact with THR 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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85D SER* 6.0 1.6 - - - +
88D VAL* 5.3 1.6 - - - +
89D SER* 5.9 6.7 - - - -
92D LEU* 4.2 11.8 - - - +
114D ALA 2.7 24.3 + - - +
115D ASN* 3.3 14.2 + - - -
117D TYR* 1.3 75.2 - - + +
119D ALA* 1.3 63.7 + - - +
121D GLU* 3.6 17.6 - - + +
122D MET* 3.2 31.5 + - - +
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Residues in contact with ALA 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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10D ILE* 4.4 7.0 - - + -
92D LEU* 4.2 23.8 - - + +
98D ALA* 5.0 2.0 - - + -
115D ASN 3.0 21.6 + - - +
116D CYS* 3.4 11.7 - - - +
117D TYR 3.2 0.2 - - - -
118D THR* 1.3 76.3 - - - +
120D MET* 1.3 53.4 + - - +
122D MET* 2.5 22.2 - - - +
124D LEU* 3.4 24.8 + - + +
126D VAL* 4.3 15.0 - - + -
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Residues in contact with MET 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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116D CYS* 3.2 20.0 - - - +
117D TYR* 3.1 31.6 + - + +
119D ALA* 1.3 75.0 - - - +
121D GLU* 1.3 59.4 + - + +
122D MET 2.9 17.3 - - - +
123D ASP* 4.0 7.3 + - - +
124D LEU 4.9 5.4 - - - +
126D VAL* 3.8 18.8 - - + -
151D VAL* 3.9 20.4 - - + +
153D ILE* 3.2 33.9 - - - -
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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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117D TYR* 2.9 27.5 + - + +
118D THR* 3.6 26.2 + - - +
120D MET* 1.3 74.3 - - + +
122D MET* 1.3 59.3 + - + +
123D ASP* 4.4 1.5 + - - +
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Residues in contact with MET 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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89D SER* 4.1 18.2 - - - +
90D ARG* 4.4 9.4 - - - +
92D LEU* 4.2 18.6 - - - +
93D ALA* 3.7 35.2 - - + -
118D THR* 3.2 17.9 + - - +
119D ALA 2.5 27.9 - - - +
120D MET 2.9 9.7 - - - +
121D GLU* 1.3 77.0 - - + +
123D ASP* 1.3 53.1 + - - +
124D LEU* 2.7 21.0 + - + -
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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