Contacts of the strand formed by residues 73 - 78 (chain A) in PDB entry 3ONC
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 PHE 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LEU* 3.9 17.7 - - + -
10A ALA* 5.0 9.0 - - + -
11A LYS 3.5 26.5 - - - -
12A MET* 3.6 32.8 - - + -
13A PRO* 3.4 24.9 - - + -
40A ARG 2.8 10.5 + - - +
41A HIS* 3.1 25.5 - + + -
42A ILE 3.2 5.7 + - - -
72A LEU* 1.3 74.0 - - - +
74A ILE* 1.3 58.9 + - - +
75A VAL* 3.7 24.2 - - + -
105A ASP* 3.4 29.8 - - + -
106A LEU* 3.8 17.5 - - + -
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Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ARG 5.1 0.2 - - - +
42A ILE* 3.8 24.5 - - + +
44A CYS* 4.3 6.7 - - - -
58A ILE* 3.8 26.9 - - + -
69A ARG* 4.2 15.5 - - - +
72A LEU* 4.1 22.7 - - + -
73A PHE* 1.3 78.5 - - - +
75A VAL* 1.3 62.1 + - - +
99A LEU* 4.0 18.4 - - + -
101A LEU* 3.8 32.8 - - + -
104A LEU* 3.9 5.2 - - + +
105A ASP* 2.9 33.9 + - - +
106A LEU 3.4 6.6 + - - +
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A MET* 4.3 1.6 - - + -
41A HIS* 3.6 26.9 - - + +
42A ILE 3.1 9.1 + - - +
43A ASP* 3.7 20.0 - - - +
44A CYS* 2.9 32.4 + - - +
73A PHE* 3.7 24.5 - - + -
74A ILE* 1.3 78.3 - - - +
76A SER* 1.3 69.6 + - - +
77A LYS* 5.2 0.7 - - + -
104A LEU* 4.9 0.2 - - - -
106A LEU* 3.3 30.3 - - + +
108A LEU* 4.1 12.3 - - + -
183A GLN* 4.8 1.3 - - - +
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Residues in contact with SER 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A CYS* 3.4 8.3 - - - -
45A ALA* 3.6 5.5 - - - -
51A GLU* 2.6 29.2 + - - -
74A ILE 4.3 0.2 - - - -
75A VAL* 1.3 77.9 - - - +
77A LYS* 1.3 75.7 + - - +
95A THR* 3.4 26.8 + - - +
99A LEU* 4.4 0.9 - - - -
104A LEU* 4.1 12.4 - - - +
106A LEU 3.1 6.9 + - - +
107A TYR* 3.3 8.8 - - - -
108A LEU 2.9 21.3 + - - -
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Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ASP* 2.7 33.0 + - - -
44A CYS 2.9 20.0 + - - +
45A ALA* 4.2 2.5 - - + +
46A HIS* 4.0 17.7 + - - +
48A TYR* 3.1 19.8 + - - -
76A SER* 1.3 92.6 + - - +
78A LEU* 1.3 62.7 + - - +
79A TRP* 3.6 2.9 + - - +
95A THR* 4.9 0.3 + - - -
107A TYR* 3.6 8.8 + - - -
108A LEU* 3.2 23.1 - - + +
110A HIS* 3.5 44.2 + - + +
159A SER* 4.8 0.4 - - - +
183A GLN* 3.3 28.5 - - - +
500A NAP 3.7 6.3 - - - +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LYS* 1.3 69.4 - - - +
79A TRP* 1.3 66.2 + - - +
80A CYS 3.9 0.2 + - - -
82A TYR* 3.7 25.8 - - + +
83A HIS* 4.0 12.5 + - + +
88A VAL* 4.1 20.9 - - + +
91A ALA* 3.7 22.0 - - + -
107A TYR* 3.5 29.5 - - + +
108A LEU 2.8 14.8 + - - +
109A ILE* 4.4 5.6 - - + -
110A HIS* 3.2 23.0 + - - +
140A THR* 3.9 28.3 - - + -
144A MET* 4.1 12.1 - - - -
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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