Contacts of the strand formed by residues 69 - 74 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ALA* 4.5 4.3 - - - -
24B PHE* 5.3 0.9 - - + -
59B ALA* 3.0 38.6 - - + +
62B TYR* 3.8 12.6 - - + -
63B ALA* 3.7 8.3 - - + +
68B PHE* 1.3 91.3 - - - +
70B ALA* 1.3 62.0 + - - +
95B PRO 3.2 5.3 + - - -
96B VAL* 3.5 5.1 - - + -
97B LEU 2.8 23.6 + - - -
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Residues in contact with ALA 70 (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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15B LEU* 3.7 26.9 - - + -
20B ALA* 4.8 1.5 - - + +
22B HIS 4.4 10.3 + - - +
23B LEU* 3.6 20.3 - - + +
24B PHE* 3.2 30.5 + - - -
59B ALA* 4.3 2.6 - - - +
68B PHE* 4.8 1.3 - - + -
69B ALA* 1.3 77.8 - - - +
71B LEU* 1.3 60.3 + - - +
96B VAL* 4.9 0.2 - - - -
97B LEU* 3.3 16.2 - - + +
99B ILE* 4.7 1.6 - - + -
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Residues in contact with LEU 71 (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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23B LEU* 4.2 1.8 - - - -
24B PHE* 3.3 8.1 - - + +
25B GLY* 4.2 1.3 - - - -
52B GLU 4.5 0.7 - - - +
55B ALA* 3.5 34.8 - - + +
56B SER* 3.8 29.2 - - - +
59B ALA* 4.5 4.5 - - + -
70B ALA* 1.3 75.2 - - - +
72B LEU* 1.3 61.4 + - - +
73B THR* 3.9 11.2 - - + -
82B ALA* 3.9 9.9 - - + -
86B ILE* 4.0 8.5 - - + -
96B VAL* 4.4 9.6 - - + -
97B LEU 2.7 13.3 + - - +
98B HIS* 3.6 29.2 - - + +
99B ILE* 2.7 35.3 + - - +
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Residues in contact with LEU 72 (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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23B LEU* 4.0 18.4 - - + -
24B PHE 2.7 14.8 + - - +
25B GLY* 3.1 21.5 - - - -
26B VAL 3.4 7.5 + - - +
31B ASN* 3.4 35.7 - - + +
34B PHE* 4.2 20.2 - - + -
35B LEU* 4.1 10.3 - - + -
46B TRP* 3.9 20.9 - - + -
71B LEU* 1.3 74.0 - - - +
73B THR* 1.3 71.4 + - - +
99B ILE* 3.3 32.1 - - + +
101B GLY* 4.3 3.1 - - - +
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Residues in contact with THR 73 (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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25B GLY* 5.4 0.2 - - - -
26B VAL 4.3 4.3 - - - -
31B ASN* 3.3 13.3 + - - +
52B GLU* 3.9 22.9 - - + -
71B LEU* 3.9 19.1 - - + -
72B LEU* 1.3 80.0 - - - +
74B THR* 1.3 59.9 + - - +
78B GLY* 3.6 17.0 - - - +
79B GLU* 3.3 14.0 + - - +
82B ALA* 4.5 0.7 - - + -
98B HIS* 2.8 32.0 + - + +
99B ILE 2.9 7.5 + - - +
100B VAL* 3.4 5.2 - - - +
101B GLY 3.0 23.2 + - - -
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Residues in contact with THR 74 (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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600A TPP 4.0 21.8 - - + -
26B VAL 4.6 1.6 + - - +
27B PRO 4.8 0.9 - - - +
28B GLY* 3.9 17.6 - - - -
29B ASP 4.4 0.7 + - - -
30B TYR* 3.8 20.3 + - - +
31B ASN* 3.8 13.4 + - - +
52B GLU* 5.1 0.6 + - - +
73B THR* 1.3 77.2 - - - +
75B PHE* 1.3 71.5 + - - +
77B VAL* 3.6 26.2 - - + -
78B GLY* 3.0 23.4 + - - +
79B GLU* 3.1 8.1 + - - +
100B VAL* 4.0 2.9 - - - -
101B GLY 4.0 2.5 - - - -
116B HIS* 4.4 4.7 - - - +
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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