Contacts of the strand formed by residues 69 - 74 (chain C) in PDB entry 1OVM
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 ALA 69 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C ALA* 4.5 3.8 - - - -
24C PHE* 5.3 0.9 - - + -
59C ALA* 3.0 38.6 - - + +
62C TYR* 3.8 14.4 - - + -
63C ALA* 3.7 6.7 - - + -
68C PHE* 1.3 90.9 - - - +
70C ALA* 1.3 56.2 + - - +
95C PRO 3.2 5.6 + - - +
96C VAL* 3.4 6.0 - - + -
97C LEU 2.8 29.1 + - - -
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 3.9 25.1 - - + -
20C ALA* 4.8 2.2 - - + +
22C HIS 4.6 9.9 + - - +
23C LEU* 3.5 22.1 - - + +
24C PHE* 3.2 30.2 + - - +
59C ALA* 4.2 3.4 - - - +
68C PHE* 4.9 1.6 - - + -
69C ALA* 1.3 77.0 - - - +
71C LEU* 1.3 60.6 + - - +
96C VAL* 4.8 0.2 - - - -
97C LEU* 3.3 16.4 - - + +
99C ILE* 4.8 1.8 - - + -
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LEU* 4.1 1.6 - - - -
24C PHE* 3.3 9.4 - - + +
25C GLY* 4.1 1.1 - - - -
52C GLU 4.5 0.9 - - - +
55C ALA* 3.5 34.8 - - + +
56C SER* 3.8 28.7 - - - +
59C ALA* 4.5 4.0 - - + -
70C ALA* 1.3 75.8 - - - +
72C LEU* 1.3 66.7 + - - +
73C THR* 3.9 15.0 - - + -
82C ALA* 3.9 15.0 - - + -
86C ILE* 4.1 7.9 - - + -
96C VAL* 4.3 9.6 - - + -
97C LEU 2.7 14.2 + - - +
98C HIS* 3.6 23.7 - - + +
99C ILE* 2.7 30.8 + - - +
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Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LEU* 3.9 24.5 - - + -
24C PHE 2.7 14.7 + - - +
25C GLY* 3.1 21.7 - - - -
26C VAL 3.4 7.1 + - - +
31C ASN* 3.5 35.0 - - + +
34C PHE* 4.3 13.0 - - + -
35C LEU* 4.0 11.0 - - + -
46C TRP* 3.9 20.6 - - + -
71C LEU* 1.3 75.5 - - - +
73C THR* 1.3 71.0 + - - +
99C ILE* 3.3 31.4 - - + +
101C GLY* 4.4 3.1 - - - +
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Residues in contact with THR 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C GLY* 5.4 0.2 - - - -
26C VAL 4.3 6.1 - - - -
31C ASN* 3.3 10.9 + - - -
52C GLU* 4.0 18.2 - - + +
71C LEU* 3.9 16.2 - - + -
72C LEU* 1.3 80.5 - - - +
74C THR* 1.3 60.1 + - - +
78C GLY* 3.6 23.1 - - - +
79C GLU* 3.3 12.5 + - - +
82C ALA* 4.5 0.4 - - + -
98C HIS* 2.8 32.7 + - + +
99C ILE 2.9 6.7 + - - +
100C VAL* 3.3 4.7 - - - +
101C GLY 3.0 22.7 + - - -
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Residues in contact with THR 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C VAL 4.6 1.4 + - - +
27C PRO 4.7 0.7 - - - +
28C GLY* 3.9 15.1 - - - -
29C ASP 4.4 0.2 + - - -
30C TYR* 3.8 23.4 + - - +
31C ASN* 3.7 14.1 - - - +
73C THR* 1.3 77.0 - - - +
75C PHE* 1.3 71.3 + - - +
77C VAL* 3.7 25.6 - - + -
78C GLY* 3.0 22.0 + - - +
79C GLU 3.1 8.0 + - - -
100C VAL* 4.0 2.7 - - - -
101C GLY 4.0 2.7 - - - -
116C HIS* 4.4 5.3 - - - +
600D TPP 4.0 23.1 - - + -
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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