Contacts of the helix formed by residues 142 - 155 (chain B) in PDB entry 3C3C
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 142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140B LYS 4.9 5.4 - - - +
141B ALA* 1.3 76.0 - - - +
143B PRO* 1.4 68.7 - - + +
144B ALA* 4.5 4.5 - - + +
145B LYS* 3.1 42.1 + - + +
146B ILE* 3.0 29.3 + - - +
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Residues in contact with PRO 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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141B ALA 4.2 3.4 - - - +
142B GLU* 1.4 88.7 - - + +
144B ALA* 1.3 52.6 + - + +
146B ILE* 3.4 9.9 + - + +
147B GLU* 2.7 35.4 + - - +
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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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142B GLU* 3.3 5.1 - - + +
143B PRO* 1.3 81.0 - - + +
145B LYS* 1.3 57.8 + - + +
147B GLU* 3.5 7.5 + - - +
148B ALA* 2.9 27.4 + - - +
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Residues in contact with LYS 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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125B VAL* 5.9 0.7 - - + -
126B GLU* 3.4 36.9 - - + +
141B ALA* 6.4 0.2 - - - -
142B GLU* 3.1 43.5 + - + +
144B ALA* 1.3 75.8 - - + +
146B ILE* 1.3 60.5 + - - +
148B ALA* 3.0 9.3 + - - +
149B PHE 2.8 24.6 + - - -
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Residues in contact with ILE 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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126B GLU* 3.8 18.2 - - + +
129B GLY* 4.2 14.1 - - - +
141B ALA* 3.7 31.0 - - + +
142B GLU 3.0 21.3 + - - +
143B PRO* 3.7 8.1 - - + +
145B LYS* 1.3 71.2 - - - +
147B GLU* 1.3 66.8 + - - +
149B PHE* 3.4 2.3 + - - +
150B ARG* 3.1 56.5 + - - +
173B SER* 4.0 7.9 - - - +
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Residues in contact with GLU 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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143B PRO 2.7 21.6 + - - +
144B ALA* 3.6 9.0 - - - +
146B ILE* 1.3 73.5 - - - +
148B ALA* 1.3 62.7 + - - +
150B ARG* 3.5 13.3 + - - +
151B ALA* 3.3 27.4 + - - +
179B ASN* 4.8 12.1 + - - -
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Residues in contact with ALA 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 2.9 15.5 + - - +
145B LYS* 3.0 12.0 + - - +
147B GLU* 1.3 75.2 - - - +
149B PHE* 1.3 63.8 + - - +
151B ALA* 3.3 6.5 + - - +
152B SER* 3.0 25.0 + - - -
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Residues in contact with PHE 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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99B VAL* 4.0 24.0 - - + -
121B LEU* 4.0 34.8 - - + -
124B HIS* 3.7 29.2 - + + -
126B GLU* 3.5 44.0 - - + +
127B GLU* 3.6 30.1 - - + -
145B LYS 2.8 10.3 + - - +
146B ILE 3.5 7.9 - - - +
148B ALA* 1.3 70.6 - - - +
150B ARG* 1.3 61.8 + - - +
152B SER* 3.2 20.0 + - - -
153B LEU* 3.2 27.1 + - + +
173B SER* 3.9 11.0 - - - -
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Residues in contact with ARG 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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146B ILE* 3.1 32.5 + - - +
147B GLU* 3.9 15.9 - - - +
148B ALA 3.2 0.2 - - - -
149B PHE* 1.3 76.9 - - - +
151B ALA* 1.3 53.3 + - - +
153B LEU* 3.4 9.7 + - - +
154B SER* 2.7 36.1 + - - -
171B ALA 5.1 2.6 + - - -
172B HIS 4.9 1.0 - - - -
173B SER* 2.7 43.5 + - - +
176B VAL* 4.1 16.2 + - - +
177B GLY* 3.5 39.3 + - - +
178B VAL* 4.9 0.7 - - - -
179B ASN* 5.1 6.1 - - - +
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Residues in contact with ALA 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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147B GLU* 3.3 24.7 + - - +
148B ALA* 3.8 6.1 - - - +
150B ARG* 1.3 75.8 - - - +
152B SER* 1.3 65.0 + - - +
154B SER* 3.6 7.1 + - - -
155B LYS* 3.1 40.9 + - - +
179B ASN* 5.7 2.0 - - - +
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Residues in contact with SER 152 (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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98B CYS 5.2 0.4 - - - -
99B VAL* 3.4 42.5 - - - -
104B GLU* 4.0 12.2 + - - +
148B ALA 3.0 14.7 + - - -
149B PHE* 3.2 12.6 + - - -
151B ALA* 1.3 76.5 - - - +
153B LEU* 1.3 62.7 + - - +
155B LYS* 3.4 13.9 + - - +
156B LEU* 3.6 16.8 - - - +
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B VAL* 4.3 7.8 - - - +
60B MET* 4.4 17.9 - - + -
99B VAL* 4.0 26.0 - - + -
118B LEU* 5.1 1.1 - - + -
121B LEU* 4.2 17.7 - - + -
149B PHE* 3.2 33.3 + - + +
150B ARG* 3.4 8.0 + - - +
151B ALA 3.3 0.2 - - - -
152B SER* 1.3 75.6 - - - +
154B SER* 1.3 58.6 - - - +
155B LYS 3.1 0.4 - - - -
156B LEU* 3.0 38.3 + - + +
157B GLY 4.3 1.2 + - - -
173B SER 4.4 4.3 - - - +
174B SER* 3.9 35.0 - - - +
178B VAL* 4.6 11.7 - - + -
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Residues in contact with SER 154 (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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150B ARG 2.7 22.5 + - - -
151B ALA* 4.0 8.3 - - - -
152B SER 3.3 0.2 - - - -
153B LEU* 1.3 76.3 - - - +
155B LYS* 1.3 61.0 + - - +
156B LEU 3.3 0.2 - - - -
157B GLY 3.4 15.6 - - - +
178B VAL* 3.6 12.7 - - - -
179B ASN* 3.1 43.5 + - - +
180B LEU* 3.4 14.3 - - - +
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Residues in contact with LYS 155 (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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17B ARG* 3.0 25.5 + - - -
104B GLU* 3.5 27.8 - - + +
108B ALA* 4.7 8.0 - - + +
151B ALA* 3.1 28.9 + - - +
152B SER* 3.7 4.5 - - - +
153B LEU 3.1 0.8 - - - -
154B SER* 1.3 77.6 - - - +
156B LEU* 1.3 58.5 + - - +
157B GLY 3.2 4.1 + - - -
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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