Contacts of the helix formed by residues 148 - 157 (chain B) in PDB entry 1OCU
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 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B SER* 5.4 1.8 + - - -
92B LEU* 3.6 9.7 - - - +
95B GLU* 2.5 27.3 + - - -
96B ILE* 5.6 0.9 - - - -
99B LEU* 4.8 1.6 - - - -
143B LEU 4.1 0.6 + - - -
144B LEU* 2.8 39.0 + - - +
145B GLN 5.3 0.9 - - - +
146B SER 3.9 0.4 - - - -
147B GLY* 1.3 71.0 - - - +
149B LYS* 1.3 60.8 + - - +
151B LEU* 3.1 25.4 + - - +
152B VAL* 3.6 22.5 + - - +
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Residues in contact with LYS 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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95B GLU* 2.7 14.9 + - - +
99B LEU* 6.5 0.9 - - - -
147B GLY 4.5 6.1 - - - +
148B SER* 1.3 71.8 - - - +
150B VAL* 1.3 65.7 + - + +
152B VAL* 3.1 9.5 + - - +
153B ARG* 3.1 21.4 + - - +
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B PHE* 3.3 27.6 - - + -
91B CME 4.0 39.3 - - + +
92B LEU* 4.1 7.6 - - + +
95B GLU* 3.1 34.9 + - + +
148B SER* 4.0 0.4 - - - +
149B LYS* 1.3 78.8 - - + +
151B LEU* 1.3 61.7 + - - +
153B ARG* 3.3 8.9 + - - +
154B PHE* 3.0 21.1 + - - +
160B PHE* 4.2 7.4 - - + -
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Residues in contact with LEU 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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36B LEU* 5.9 0.2 - - + -
71B PHE* 4.7 15.0 - - + -
88B PHE* 3.8 13.0 - - + -
92B LEU* 5.0 2.9 - - + -
135B MET* 3.8 29.2 - - + -
138B VAL* 3.9 17.3 - - + -
139B ALA* 4.2 20.2 - - + +
144B LEU* 3.6 37.0 - - + +
145B GLN* 4.2 7.2 - - - +
148B SER* 3.1 21.3 + - - +
150B VAL* 1.3 78.4 - - - +
152B VAL* 1.3 65.6 + - + +
154B PHE* 3.2 3.5 + - - +
155B ILE* 3.2 29.7 + - + +
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Residues in contact with VAL 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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70B SER* 3.6 34.3 - - - +
71B PHE* 3.9 29.6 - - + -
72B HIS* 4.0 9.4 - - + -
145B GLN 5.4 0.4 - - - +
148B SER 3.6 14.8 + - - +
149B LYS* 3.1 10.6 + - - +
151B LEU* 1.3 75.8 - - + +
153B ARG* 1.3 60.8 + - - +
155B ILE* 3.1 4.0 + - - +
156B GLU* 2.8 55.7 + - - +
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Residues in contact with ARG 153 (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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80B ARG* 3.7 1.7 + - - -
91B CME 4.8 10.0 + - - -
149B LYS 3.1 10.3 + - - +
150B VAL* 3.6 10.1 - - - +
152B VAL* 1.3 80.7 - - - +
154B PHE* 1.3 60.9 + - - +
156B GLU* 4.5 1.8 - - - +
157B ALA* 3.1 39.6 + - + +
159B LYS 3.5 8.1 + - - -
160B PHE* 3.0 41.5 + - + -
162B GLY* 3.1 32.3 - - - +
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Residues in contact with PHE 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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62B ILE* 5.1 4.1 - - + +
78B VAL* 3.9 4.5 - - - +
80B ARG* 2.9 54.6 + - + -
84B ASP 3.6 10.5 - - - -
85B PHE* 3.9 42.4 - + - -
88B PHE* 3.5 65.3 - + + -
135B MET* 3.9 16.4 - - + -
150B VAL 3.0 6.2 + - - +
151B LEU 3.2 5.3 + - - +
153B ARG* 1.3 75.8 - - - +
155B ILE* 1.3 60.4 + - + +
160B PHE* 3.6 24.0 - + + -
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Residues in contact with ILE 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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38B ILE* 3.2 31.0 - - + -
62B ILE* 4.1 12.1 - - + +
64B CYS* 3.6 33.0 - - + -
71B PHE* 3.8 21.5 - - + -
76B SER* 3.5 17.4 - - - +
78B VAL* 3.4 24.5 - - - +
135B MET* 3.6 19.1 - - + -
139B ALA* 5.6 1.1 - - + -
151B LEU* 3.2 20.4 - - + +
152B VAL 3.1 6.9 + - - +
154B PHE* 1.3 82.8 - - + +
156B GLU* 1.3 57.3 + - - +
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Residues in contact with GLU 156 (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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71B PHE* 3.3 20.3 - - + +
72B HIS* 2.7 55.5 + - - +
73B LYS* 3.5 33.5 + - - +
76B SER* 3.4 20.4 + - - +
78B VAL* 3.6 8.2 - - - +
152B VAL* 2.8 32.6 + - - +
153B ARG* 5.0 1.3 - - - -
155B ILE* 1.3 74.4 - - - +
157B ALA* 1.3 67.1 + - - +
158B GLU* 3.6 1.9 + - - -
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Residues in contact with ALA 157 (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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78B VAL* 3.3 7.8 - - - +
80B ARG* 2.7 26.4 + - - +
153B ARG* 3.1 40.9 + - + +
156B GLU* 1.3 76.0 - - - +
158B GLU* 1.3 62.2 + - - +
159B LYS 3.5 20.2 - - - +
160B PHE 4.7 0.4 - - - +
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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