Contacts of the strand formed by residues 53 - 60 (chain A) in PDB entry 1OLN
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 ILE 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLN* 4.0 39.3 - - + +
13A LEU 4.6 0.2 - - - +
14A PRO* 4.1 28.3 - - + -
51A GLY 5.4 1.6 - - - +
52A MET* 1.3 72.6 - - - +
54A LEU* 1.3 60.1 + - - +
73A PRO* 3.0 22.4 - - - +
74A PRO* 3.4 11.3 - - + +
77A PHE* 3.3 31.7 - - + -
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Residues in contact with LEU 54 (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 GLN* 4.3 2.2 - - - -
13A LEU* 2.9 34.8 + - - +
15A ALA* 3.4 25.8 - - + +
42A PHE* 3.9 7.6 - - + -
46A THR* 3.5 28.5 - - + -
49A LYS* 4.3 17.5 - - + +
52A MET* 3.3 20.2 - - + +
53A ILE* 1.3 74.1 - - - +
55A PRO* 1.3 67.8 - - + +
56A VAL 3.7 0.5 + - - -
70A ILE* 3.5 31.6 - - + -
71A LYS 3.8 9.6 - - - +
73A PRO* 4.3 7.6 - - + -
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Residues in contact with PRO 55 (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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11A LEU 3.3 11.9 - - - +
12A GLN* 3.8 20.6 - - + +
54A LEU* 1.3 85.4 - - + +
56A VAL* 1.3 59.4 + - - +
57A VAL* 5.7 0.7 - - + -
70A ILE* 4.0 1.3 - - - -
71A LYS* 3.0 41.5 + - + +
72A THR 3.2 30.5 - - - +
73A PRO* 3.7 6.7 - - + -
74A PRO* 3.8 12.8 - - + -
1060C U 4.6 7.6 - - - +
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Residues in contact with VAL 56 (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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10A LYS* 3.5 2.1 - - - +
11A LEU* 2.9 36.8 + - + +
13A LEU* 3.4 34.1 - - + -
38A PHE* 3.8 7.2 - - + -
42A PHE* 3.7 16.6 - - + -
55A PRO* 1.3 75.0 - - - +
57A VAL* 1.3 66.6 + - - +
58A ILE* 3.8 1.9 + - + +
68A PHE* 3.3 42.4 - - + -
69A ILE 3.2 12.6 - - - +
70A ILE* 4.1 3.8 - - + -
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Residues in contact with VAL 57 (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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8A GLN* 3.9 33.7 - - + +
9A ILE 3.7 6.1 - - - +
10A LYS* 4.1 20.9 - - + +
55A PRO* 5.7 0.9 - - + -
56A VAL* 1.3 75.5 - - - +
58A ILE* 1.3 60.8 + - - +
59A THR* 3.7 4.2 + - - +
68A PHE* 3.2 19.9 - - - -
69A ILE* 2.9 28.7 + - + +
71A LYS* 4.1 27.1 - - + +
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Residues in contact with ILE 58 (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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8A GLN* 3.3 6.6 - - - +
9A ILE* 2.7 63.3 + - + +
11A LEU* 5.1 0.2 - - + -
28A LEU* 4.1 11.2 - - + -
33A VAL* 4.5 1.6 - - + -
38A PHE* 3.3 59.2 - - + -
56A VAL* 3.8 4.1 + - + -
57A VAL* 1.3 73.1 - - - +
59A THR* 1.3 68.6 + - - +
60A VAL* 4.4 14.1 - - + +
66A PHE* 3.8 13.7 - - + -
67A THR 3.5 2.2 - - - +
68A PHE* 3.4 17.3 - - + -
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Residues in contact with THR 59 (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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8A GLN* 3.0 41.7 + - + +
57A VAL* 3.7 6.6 + - - +
58A ILE* 1.3 74.6 - - - +
60A VAL* 1.3 64.4 + - - +
61A TYR* 4.0 19.1 + - + +
66A PHE* 3.0 26.3 - - - +
67A THR* 2.8 26.5 + - - -
68A PHE* 5.0 0.5 - - - -
69A ILE* 6.1 0.5 - - - +
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Residues in contact with VAL 60 (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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8A GLN* 4.1 20.9 + - - +
9A ILE* 5.1 4.5 - - + -
31A HIS* 4.5 24.7 - - + +
32A GLY* 4.8 0.4 - - - -
33A VAL* 3.3 40.6 - - + +
58A ILE* 4.4 2.9 - - + -
59A THR* 1.3 74.8 - - - +
61A TYR* 1.3 67.1 + - - +
62A GLU 4.1 0.3 + - - -
64A LYS* 4.3 4.3 - - - +
65A SER 3.3 7.0 - - - +
66A PHE* 3.6 17.9 - - + -
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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