Contacts of the helix formed by residues 109 - 122 (chain A) 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 GLU 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A HIS* 3.9 38.0 + - + +
103A ASP* 5.8 1.2 - - - +
106A GLN* 4.4 15.2 - - - +
107A GLY 3.5 14.5 - - - +
108A VAL* 1.3 79.0 - - - +
110A ALA* 1.3 59.9 + - - +
111A GLN* 3.2 21.7 + - + +
112A THR* 2.9 35.9 + - + -
113A LEU* 3.4 7.1 + - - +
409A LEU* 6.0 2.0 - - - -
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Residues in contact with ALA 110 (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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109A GLU* 1.3 70.0 - - - +
111A GLN* 1.3 61.2 + - - +
112A THR 3.2 0.4 - - - -
113A LEU* 3.0 35.8 + - + +
114A ALA* 3.3 14.7 + - - +
407A HIS* 5.3 2.7 - - + +
408A MET* 5.7 0.2 - - - -
409A LEU* 4.4 12.6 - - + +
467A SER* 3.1 35.7 + - - +
468A LEU 5.4 1.6 - - - +
469A ASP* 4.4 16.4 - - + +
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Residues in contact with GLN 111 (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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10A ILE* 5.2 0.2 - - - +
11A ALA 5.4 0.4 - - - +
12A HIS* 3.1 43.2 + - + -
80A GLY* 3.3 30.7 - - - +
81A HIS* 6.3 0.7 - - - +
109A GLU* 3.3 17.5 + - + +
110A ALA* 1.3 88.2 + - - +
112A THR* 1.3 66.1 + - + +
113A LEU 3.7 0.2 + - - -
114A ALA* 4.3 2.8 + - - +
115A ASN* 4.2 14.2 + - - -
467A SER* 4.5 9.2 - - - -
469A ASP* 5.4 3.8 - - - -
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Residues in contact with THR 112 (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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10A ILE* 3.8 19.6 - - + +
11A ALA* 3.2 39.7 - - - +
12A HIS* 4.3 9.4 - - + +
100A LEU* 4.2 11.7 - - + +
101A VAL 5.6 0.9 - - - +
102A VAL* 5.9 0.2 - - - +
108A VAL* 3.6 19.2 - - - +
109A GLU* 2.9 21.2 + - + +
111A GLN* 1.3 80.8 - - + +
113A LEU* 1.3 60.1 + - - +
115A ASN 4.2 0.7 - - - -
116A CYS* 3.0 30.5 + - - +
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Residues in contact with LEU 113 (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 VAL* 3.9 14.8 - - + -
109A GLU 3.9 5.4 - - - +
110A ALA* 3.0 29.4 + - + +
112A THR* 1.3 76.4 + - - +
114A ALA* 1.3 67.3 + - - +
116A CYS* 3.0 3.4 + - - +
117A TYR* 2.9 59.0 + - + +
150A ILE* 3.8 19.3 - - + -
151A VAL* 3.5 31.2 - - + -
409A LEU* 4.1 22.7 - - + -
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Residues in contact with ALA 114 (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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80A GLY 5.9 1.3 - - - +
82A VAL* 3.9 15.5 - - + -
110A ALA 3.3 6.1 + - - +
111A GLN 4.5 4.7 - - - +
113A LEU* 1.3 79.2 - - - +
115A ASN* 1.3 62.7 + - - +
117A TYR* 3.4 11.0 + - - +
118A THR* 2.8 25.6 + - - +
469A ASP* 3.3 37.6 + - - +
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Residues in contact with ASN 115 (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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10A ILE* 3.9 28.8 - - + +
78A THR* 3.4 15.3 - - + +
79A PRO 3.0 27.1 + - - -
80A GLY* 4.0 13.6 - - - +
81A HIS 5.3 2.9 - - - +
82A VAL* 5.5 2.6 - - - +
85A SER* 6.0 0.3 - - - -
88A VAL* 3.4 24.9 - - + +
92A LEU* 4.3 4.2 - - + +
111A GLN 4.2 7.9 + - - +
112A THR 3.9 2.1 + - - +
113A LEU 3.3 0.2 - - - -
114A ALA* 1.3 81.5 - - - +
116A CYS* 1.3 60.4 + - - +
118A THR* 3.2 6.6 + - - -
119A ALA* 3.0 29.6 + - - +
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Residues in contact with CYS 116 (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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10A ILE* 4.2 11.4 - - - +
100A LEU* 3.7 36.8 - - - -
112A THR 3.0 21.5 + - - +
113A LEU* 3.0 8.6 + - - +
115A ASN* 1.3 77.2 - - - +
117A TYR* 1.3 64.1 + - + +
119A ALA* 3.4 3.0 + - - +
120A MET* 3.1 29.1 + - - +
126A VAL* 4.3 15.2 - - - +
151A VAL* 3.8 23.8 - - + -
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Residues in contact with TYR 117 (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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113A LEU* 2.9 57.6 + - + +
114A ALA* 3.9 7.9 - - - +
116A CYS* 1.3 75.7 - - + +
118A THR* 1.3 60.7 + - + +
120A MET* 3.1 28.4 + - + +
121A GLU* 2.8 41.4 + - + +
150A ILE* 3.2 27.8 + - - +
151A VAL* 4.4 9.4 - - + -
407A HIS* 5.9 9.6 - + + -
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Residues in contact with THR 118 (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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85A SER* 6.1 0.9 - - - +
88A VAL* 5.2 1.8 - - - +
89A SER* 5.9 7.4 - - - -
92A LEU* 4.4 11.7 - - - +
114A ALA 2.8 18.4 + - - +
115A ASN* 3.2 14.7 + - - -
117A TYR* 1.3 74.4 - - + +
119A ALA* 1.3 63.6 + - - +
121A GLU* 3.3 20.6 + - - +
122A MET* 3.1 35.6 + - + +
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Residues in contact with ALA 119 (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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10A ILE* 4.3 12.1 - - + -
92A LEU* 4.1 25.0 - - + +
98A ALA* 4.9 2.7 - - + -
115A ASN 3.0 18.2 + - - +
116A CYS 3.6 6.5 - - - +
117A TYR 3.3 0.2 - - - -
118A THR* 1.3 76.2 - - - +
120A MET* 1.3 54.2 + - - +
122A MET* 2.6 20.8 - - - +
124A LEU* 3.2 29.3 + - + +
126A VAL* 4.4 11.9 - - + -
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Residues in contact with MET 120 (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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116A CYS 3.1 9.6 + - - +
117A TYR* 3.1 40.6 + - + +
119A ALA* 1.3 74.8 - - - +
121A GLU* 1.3 58.8 + - - +
122A MET 2.8 14.9 - - - +
123A ASP* 4.5 6.4 - - - +
124A LEU 4.8 4.0 - - - +
126A VAL* 3.9 17.7 - - + -
151A VAL* 3.6 27.1 - - + +
153A ILE* 3.5 31.0 - - + -
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Residues in contact with GLU 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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117A TYR* 2.8 23.8 + - + +
118A THR* 3.3 31.6 - - - +
120A MET* 1.3 75.5 - - - +
122A MET* 1.3 62.1 + - + +
123A ASP* 3.8 6.4 + - - +
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Residues in contact with MET 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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89A SER* 3.8 14.1 - - - +
90A ARG* 3.8 12.8 - - - +
92A LEU* 4.0 26.9 - - - -
93A ALA* 3.7 33.9 - - + -
118A THR* 3.1 19.4 + - + +
119A ALA 2.6 24.6 - - - +
120A MET 2.8 9.7 - - - +
121A GLU* 1.3 75.7 - - + +
123A ASP* 1.3 60.4 + - - +
124A LEU* 2.8 11.6 + - + -
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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