Contacts of the strand formed by residues 69 - 74 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ALA* 4.6 3.4 - - - -
24A PHE* 5.4 1.3 - - + -
59A ALA* 3.0 39.3 - - + +
62A TYR* 3.9 11.7 - - + -
63A ALA* 3.7 9.4 - - + +
68A PHE* 1.3 90.8 - - - +
70A ALA* 1.3 62.0 + - - +
95A PRO 3.2 5.5 + - - -
96A VAL* 3.4 5.4 - - + -
97A LEU 2.8 23.3 + - - -
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Residues in contact with ALA 70 (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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15A LEU* 3.9 27.8 - - + -
20A ALA* 4.8 1.8 - - + +
22A HIS 4.6 9.3 + - - +
23A LEU* 3.5 20.3 - - + -
24A PHE* 3.2 29.8 + - - -
59A ALA* 4.2 3.9 - - - +
68A PHE* 4.9 0.9 - - + -
69A ALA* 1.3 77.6 - - - +
71A LEU* 1.3 61.3 + - - +
96A VAL* 4.8 0.2 - - - -
97A LEU* 3.3 14.8 - - + +
99A ILE* 4.7 2.9 - - + -
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Residues in contact with LEU 71 (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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23A LEU* 4.1 2.0 - - - -
24A PHE 3.3 8.3 - - - +
25A GLY* 4.1 0.9 - - - -
52A GLU 4.5 0.9 - - - +
55A ALA* 3.5 34.1 - - + +
56A SER* 3.8 28.0 - - - +
59A ALA* 4.5 3.6 - - + -
70A ALA* 1.3 75.0 - - - +
72A LEU* 1.3 62.5 + - - +
73A THR* 3.9 14.8 - - + -
82A ALA* 3.9 14.6 - - + -
86A ILE* 4.1 9.6 - - + -
96A VAL* 4.3 9.9 - - + -
97A LEU 2.7 13.5 + - - +
98A HIS* 3.7 22.9 - - + +
99A ILE* 2.7 35.9 + - - +
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Residues in contact with LEU 72 (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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23A LEU* 4.0 18.2 - - + -
24A PHE 2.7 14.3 + - - +
25A GLY* 3.1 21.0 - - - -
26A VAL 3.4 5.6 + - - +
31A ASN* 3.5 36.1 - - + +
34A PHE* 4.2 19.5 - - + -
35A LEU* 4.1 8.7 - - + -
46A TRP* 3.9 20.6 - - + -
71A LEU* 1.3 75.7 - - - +
73A THR* 1.3 70.4 - - - +
99A ILE* 3.2 32.3 - - + +
101A GLY 4.3 2.7 - - - +
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Residues in contact with THR 73 (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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25A GLY* 5.3 0.2 - - - -
26A VAL 4.3 5.6 - - - +
31A ASN* 3.3 12.3 + - - -
52A GLU* 3.9 25.4 - - + -
71A LEU* 3.9 17.3 - - + -
72A LEU* 1.3 79.9 - - - +
74A THR* 1.3 60.9 + - - +
78A GLY* 3.6 15.5 - - - +
79A GLU* 3.3 12.6 + - - +
82A ALA* 4.5 0.9 - - + -
98A HIS* 2.8 31.7 + - + +
99A ILE 2.9 7.1 + - - +
100A VAL* 3.3 5.0 - - - +
101A GLY 3.0 23.7 + - - -
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Residues in contact with THR 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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26A VAL 4.6 1.2 + - - +
27A PRO 4.8 0.9 - - - +
28A GLY* 3.9 13.9 - - - -
29A ASP 4.5 0.2 + - - -
30A TYR* 3.8 22.3 + - - +
31A ASN* 3.8 13.9 - - - +
52A GLU* 5.2 0.6 + - - +
73A THR* 1.3 77.4 - - - +
75A PHE* 1.3 71.9 + - - +
77A VAL* 3.5 28.3 - - + -
78A GLY* 3.0 21.4 + - - +
79A GLU 3.1 8.7 + - - -
100A VAL* 3.9 3.3 - - - +
101A GLY 4.0 2.9 - - - -
116A HIS* 4.3 5.6 - - + -
600B TPP 4.0 21.1 - - + -
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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