Contacts of the helix formed by residues 144 - 155 (chain E) in PDB entry 3DCG
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 144 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76D TYR* 3.4 6.7 - - - -
80D LYS* 5.8 1.8 - - - +
112D CYS* 3.6 16.8 - - - -
142E VAL 3.7 1.0 + - - -
143E GLY* 1.3 74.5 - - - +
145E LEU* 1.3 64.9 + - - +
146E GLN* 3.7 7.8 + - - +
147E TYR* 3.1 24.8 + - - +
148E LEU* 3.0 19.8 + - - +
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Residues in contact with LEU 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D LYS 5.3 0.2 - - - +
73D VAL* 4.0 25.1 - - + -
76D TYR* 3.4 27.8 + - + -
93D PHE* 3.9 23.1 - - + -
95D ILE* 4.5 3.8 - - + -
103D LEU* 3.7 39.7 - - + +
107D ALA* 3.7 21.5 - - + -
112D CYS* 2.8 29.9 + - - +
144E SER* 1.3 71.6 - - - +
146E GLN* 1.3 56.6 + - - +
148E LEU* 4.4 2.9 - - + -
149E ALA* 2.8 29.5 + - - +
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Residues in contact with GLN 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LEU* 4.2 19.9 - - + +
107D ALA* 3.4 27.0 + - + -
108D ASN* 3.7 31.7 + - + +
111D ASP* 4.3 9.3 + - - +
112D CYS 2.8 25.7 + - - +
144E SER* 3.1 7.4 + - - +
145E LEU* 1.3 73.8 - - - +
147E TYR* 1.3 66.0 + - - +
149E ALA* 3.5 2.6 + - - +
150E LEU* 3.0 25.3 + - - +
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Residues in contact with TYR 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E GLY* 4.4 13.0 - - - -
144E SER* 3.1 22.6 + - - +
146E GLN* 1.3 78.5 - - - +
148E LEU* 1.3 76.3 + - + +
150E LEU* 3.4 7.6 + - + +
151E ALA* 2.9 40.7 + - + +
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Residues in contact with LEU 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D TYR* 3.8 19.5 - - + -
79D TYR* 4.5 8.7 - - + +
93D PHE* 4.1 31.6 - - + +
95D ILE* 3.8 15.3 - - + +
142E VAL* 5.0 0.7 - - + -
143E GLY* 3.7 22.4 - - - +
144E SER 3.0 13.1 + - - +
145E LEU* 3.8 6.1 - - - +
147E TYR* 1.3 93.0 - - + +
149E ALA* 1.3 58.2 + - - +
151E ALA* 3.2 7.6 + - + +
152E ALA* 3.0 27.9 + - - +
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Residues in contact with ALA 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ILE* 3.8 9.5 - - - +
100D ALA* 3.6 16.8 - - - +
103D LEU* 4.1 13.5 - - + -
104D LEU* 3.6 35.4 - - - +
145E LEU 2.8 21.2 + - - +
146E GLN 3.8 1.8 - - - +
148E LEU* 1.3 73.2 - - - +
150E LEU* 1.3 60.4 + - - +
152E ALA* 3.2 6.9 + - - +
153E LEU* 3.1 18.3 + - - +
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Residues in contact with LEU 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LEU* 4.4 16.1 - - + +
146E GLN 3.0 18.2 + - - +
147E TYR* 3.9 7.0 - - + +
149E ALA* 1.3 72.3 - - - +
151E ALA* 1.3 61.3 + - - +
153E LEU* 3.1 23.7 + - + +
154E ILE* 3.0 48.1 + - + +
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Residues in contact with ALA 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E TYR* 2.9 33.3 + - + +
148E LEU* 3.2 10.3 + - + +
150E LEU* 1.3 75.4 - - - +
152E ALA* 1.3 56.7 + - - +
154E ILE* 3.1 9.4 + - + +
155E LYS* 3.0 46.9 + - - +
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Residues in contact with ALA 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ILE* 3.8 39.9 - - + +
97D PRO* 4.2 17.1 - - + +
100D ALA* 4.0 7.4 - - + -
148E LEU 3.0 12.7 + - - +
149E ALA 3.4 10.3 - - - +
150E LEU 3.2 0.2 - - - -
151E ALA* 1.3 76.3 - - - +
153E LEU* 1.3 60.2 + - - +
154E ILE 3.6 0.2 + - - -
155E LYS* 4.2 17.9 + - - +
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Residues in contact with LEU 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D PRO* 4.5 7.4 - - + +
100D ALA* 3.8 24.0 - - + -
101D LEU* 3.9 40.2 - - + +
104D LEU* 4.1 16.2 - - + -
149E ALA 3.1 7.5 + - - +
150E LEU* 3.1 18.3 + - + +
152E ALA* 1.3 76.7 - - - +
154E ILE* 1.3 69.5 + - + +
155E LYS 3.7 1.7 - - - +
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Residues in contact with ILE 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E LEU* 3.0 40.8 + - + +
151E ALA* 3.1 9.1 + - - +
153E LEU* 1.3 85.5 - - + +
155E LYS* 1.3 67.4 + - + +
156E PRO* 3.0 15.9 - - + +
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Residues in contact with LYS 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D GLU* 4.6 16.7 + - - -
151E ALA* 3.0 30.1 + - - +
152E ALA* 4.2 13.4 + - - +
153E LEU 3.7 2.0 - - - +
154E ILE* 1.3 75.5 - - + +
156E PRO* 1.4 71.2 - - + +
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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