Contacts of the helix formed by residues 139 - 151 (chain B) 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 ASP 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B ALA 2.6 15.7 + - - +
137B ALA 4.2 4.7 - - - +
138B ALA* 1.3 75.4 - - - +
140B PRO* 1.3 67.3 - - - +
141B GLU* 4.4 2.6 + - - +
142B ARG* 3.3 52.4 + - - +
143B VAL* 3.1 22.9 + - - +
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Residues in contact with PRO 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ALA* 4.3 11.2 - - + -
130B LEU* 4.1 12.2 - - + +
133B ILE* 4.4 18.6 - - + -
138B ALA* 3.8 7.4 - - + +
139B ASP* 1.3 88.7 - - - +
141B GLU* 1.3 63.6 + - - +
143B VAL* 3.2 3.6 + - + +
144B ALA* 2.8 31.7 + - - +
160B ARG* 3.5 40.8 - - - +
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ASP* 3.6 3.2 + - - +
140B PRO* 1.3 85.4 - - - +
142B ARG* 1.3 58.1 + - - +
144B ALA* 3.3 7.5 + - - +
145B GLU* 3.1 37.5 + - - +
160B ARG* 2.7 40.2 + - - +
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Residues in contact with ARG 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ALA 4.9 1.4 + - - -
105B GLY 5.4 5.3 - - - -
106B GLN 4.5 11.1 + - - -
137B ALA 5.3 2.8 + - - -
139B ASP* 3.3 47.0 + - - +
140B PRO 3.3 0.4 - - - -
141B GLU* 1.3 79.1 - - - +
143B VAL* 1.3 79.7 + - - +
145B GLU* 3.6 15.9 + - - +
146B GLU* 2.7 58.1 + - - +
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B VAL* 3.6 30.5 - - + -
103B ASP 4.1 5.4 - - - +
104B ALA* 3.4 24.0 - - - +
106B GLN 4.9 0.2 - - - -
107B GLY* 4.1 13.5 - - - +
130B LEU* 3.8 15.0 - - + -
139B ASP 3.1 19.5 + - - +
140B PRO 3.7 3.1 - - - +
142B ARG* 1.3 97.2 - - - +
144B ALA* 1.3 59.8 + - - +
146B GLU* 3.3 9.2 - - + +
147B ILE* 3.1 25.8 + - - +
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LEU* 4.4 11.9 - - + +
140B PRO 2.8 17.2 + - - +
141B GLU* 3.6 8.7 - - - +
143B VAL* 1.3 75.6 - - - +
145B GLU* 1.3 62.5 + - - +
147B ILE* 3.3 13.9 + - - +
148B GLU* 3.2 23.2 + - - +
155B ALA* 4.2 25.5 - - + +
156B THR* 5.7 2.2 - - + -
160B ARG* 5.9 1.3 - - - +
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Residues in contact with GLU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B GLU* 3.1 23.9 + - - +
142B ARG* 3.6 17.7 - - - +
143B VAL 3.3 0.2 - - - -
144B ALA* 1.3 73.2 - - - +
146B GLU* 1.3 56.5 + - - +
148B GLU* 3.3 5.0 + - - +
149B ASP* 2.8 40.8 + - + +
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLN 4.9 1.0 - - - +
107B GLY* 3.6 4.3 - - - -
108B VAL* 3.3 36.1 + - + +
142B ARG* 2.7 49.1 + - - +
143B VAL* 3.3 11.9 - - + +
145B GLU* 1.3 78.9 - - - +
147B ILE* 1.3 57.9 + - + +
149B ASP* 4.5 3.1 - - - -
150B ILE* 3.0 48.7 + - + +
438B GLN* 5.0 12.6 + - - -
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Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LEU* 4.4 8.1 - - + -
102B VAL* 3.9 32.8 - - + -
108B VAL* 5.3 5.4 - - + -
128B PRO* 4.6 9.6 - - + -
129B VAL 5.7 0.7 - - - +
130B LEU* 4.0 21.3 - - + -
143B VAL 3.1 17.0 + - - +
144B ALA* 3.5 11.2 - - - +
145B GLU 3.2 0.2 - - - -
146B GLU* 1.3 77.3 - - + +
148B GLU* 1.3 57.4 + - - +
151B VAL* 2.7 51.0 + - + +
152B GLY 3.2 0.9 + - - -
153B ILE* 3.7 30.5 - - + +
155B ALA* 4.1 12.8 - - + -
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Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ALA 3.2 12.0 + - - +
145B GLU* 4.0 5.2 - - - +
147B ILE* 1.3 78.8 - - - +
149B ASP* 1.3 61.6 + - - +
152B GLY* 3.3 19.3 - - - -
153B ILE 3.3 20.9 - - - +
154B ASP* 3.5 16.9 - - - +
155B ALA* 3.1 25.3 + - - +
156B THR* 4.1 12.8 + - - +
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Residues in contact with ASP 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B GLU* 2.8 24.4 + - + +
146B GLU* 4.2 4.3 - - - +
148B GLU* 1.3 76.0 - - - +
150B ILE* 1.3 63.1 + - + +
152B GLY* 4.6 1.4 + - - -
434B TYR 5.0 1.1 - - - +
435B HIS* 3.7 36.2 + - + +
436B GLY 4.5 4.7 + - - -
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Residues in contact with ILE 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B VAL* 3.7 20.2 - - + +
113B LEU* 3.9 33.9 - - + -
117B TYR* 3.8 14.4 + - - +
146B GLU* 3.0 33.3 + - + +
149B ASP* 1.3 79.7 - - + +
151B VAL* 1.3 64.4 + - - +
152B GLY 3.4 0.4 + - - -
409B LEU* 4.6 15.7 - - + -
435B HIS* 3.5 46.5 + - + +
438B GLN* 5.3 6.3 - - + +
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LEU* 4.2 19.3 - - + -
108B VAL* 4.4 7.4 - - + -
113B LEU* 3.7 24.9 - - + -
116B CYS* 3.7 25.1 - - + -
117B TYR* 4.4 8.1 - - + -
120B MET* 3.4 29.0 - - + +
147B ILE* 2.7 29.9 + - + +
150B ILE* 1.3 74.1 - - + +
152B GLY* 1.3 55.9 + - - +
153B ILE* 3.9 20.2 - - + +
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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