Contacts of the helix formed by residues 142 - 151 (chain B) in PDB entry 5KOQ
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 PRO 142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B SER* 3.5 26.2 - - - +
106B GLN* 3.8 2.0 - - - +
129B GLY 4.6 3.6 - - - +
131B GLY 3.8 13.9 - - - +
132B PHE 3.9 1.6 - - - +
133B ILE* 3.6 33.2 - - + +
140B VAL 3.5 5.2 - - - +
141B THR* 1.4 90.4 - - + +
143B ILE* 1.3 65.3 + - - +
144B PHE* 3.4 2.9 - - + +
145B ASP* 3.3 33.8 + - - +
146B ASN* 3.1 18.4 + - - +
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Residues in contact with ILE 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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44B VAL* 3.9 12.0 - - + +
97B ILE* 3.7 30.3 - - + -
99B VAL* 3.8 17.9 - - + -
104B VAL* 3.8 17.3 - - + -
106B GLN* 3.2 31.2 + - + +
128B VAL* 3.5 30.5 - - + -
129B GLY 4.0 10.8 + - - +
130B MET* 4.3 7.9 - - + -
142B PRO* 1.3 73.0 - - - +
144B PHE* 1.3 62.7 + - - +
146B ASN* 3.1 4.0 + - - +
147B ILE* 2.9 37.7 + - + +
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Residues in contact with PHE 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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129B GLY 5.2 0.2 + - - -
130B MET* 4.1 27.1 - - + +
131B GLY 5.9 0.9 - - - +
142B PRO* 3.4 1.8 - - + +
143B ILE* 1.3 82.3 - - - +
145B ASP* 1.3 60.2 + - - +
147B ILE* 3.7 9.4 - - + +
148B ILE* 2.9 57.6 + - + +
153B LEU* 3.6 26.7 - - + -
156B ASP 3.8 11.9 - - - -
157B VAL 3.4 31.2 - - - -
158B PHE* 3.6 37.2 - + + -
178B LEU* 4.2 13.0 - - + -
329B ARG* 3.9 15.5 - - + +
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Residues in contact with ASP 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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131B GLY 4.1 1.4 - - - +
133B ILE* 4.4 12.4 + - - +
141B THR* 3.8 15.2 - - + +
142B PRO* 3.3 37.6 + - - +
144B PHE* 1.3 78.5 - - - +
146B ASN* 1.3 60.3 + - - +
148B ILE* 3.6 10.1 + - - +
149B SER* 3.1 26.4 + - - -
329B ARG* 2.8 40.8 + - - -
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Residues in contact with ASN 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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104B VAL* 3.6 18.1 - - + +
105B THR 3.5 15.9 + - - -
106B GLN* 2.8 27.3 + - - +
107B MET* 4.9 4.6 - - - +
141B THR* 3.4 28.5 + - - +
142B PRO 3.1 8.9 + - - -
143B ILE 3.1 8.7 + - - +
145B ASP* 1.3 75.0 - - - +
147B ILE* 1.3 64.1 + - - +
149B SER* 3.4 21.8 + - - -
150B GLN* 3.7 11.1 + - - +
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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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99B VAL* 4.9 4.5 - - + -
102B ILE* 4.1 27.8 - - + -
104B VAL* 4.0 21.1 - - + -
143B ILE* 2.9 39.0 + - + +
144B PHE* 3.8 11.7 - - + +
145B ASP 3.3 0.2 - - - -
146B ASN* 1.3 74.6 - - - +
148B ILE* 1.3 66.1 + - - +
150B GLN* 3.0 23.6 + - - +
151B GLY 3.8 1.7 + - - -
152B VAL* 4.5 7.5 + - + +
153B LEU* 3.6 34.5 - - + +
178B LEU* 4.3 19.5 - - + -
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Residues in contact with ILE 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 PHE* 2.9 55.2 + - + +
145B ASP* 3.6 10.8 - - - +
147B ILE* 1.3 71.5 - - - +
149B SER* 1.3 64.8 + - - +
151B GLY* 3.1 16.5 + - - -
153B LEU* 4.5 4.2 - - + +
156B ASP* 3.5 37.7 - - + +
329B ARG* 4.2 25.8 - - + +
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Residues in contact with SER 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 ASP 3.1 14.0 + - - -
146B ASN* 3.4 16.9 + - - -
147B ILE 3.2 0.6 - - - -
148B ILE* 1.3 79.1 - - - +
150B GLN* 1.3 61.3 + - - +
151B GLY* 3.2 1.1 + - - -
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Residues in contact with GLN 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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102B ILE* 4.3 9.1 - - - +
103B THR 3.0 27.8 + - - +
104B VAL* 3.4 24.0 - - - +
105B THR 4.8 0.3 + - - -
146B ASN 3.7 8.7 + - - +
147B ILE* 3.0 14.2 + - - +
149B SER* 1.3 77.9 - - - +
151B GLY* 1.3 62.7 + - - +
152B VAL* 3.5 31.7 + - + +
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Residues in contact with GLY 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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4B GLY* 3.3 22.2 + - - -
147B ILE 3.8 0.4 + - - -
148B ILE 3.1 15.5 + - - -
149B SER 3.2 2.5 - - - -
150B GLN* 1.3 79.3 - - - +
152B VAL* 1.3 61.3 + - - +
153B LEU 3.8 1.3 - - - -
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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