Contacts of the strand formed by residues 58 - 65 (chain A) in PDB entry 5LOH
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 LEU 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A VAL* 4.7 5.2 - - + -
51A LEU* 3.8 30.5 - - + -
52A GLY 3.5 13.2 - - - +
53A GLN* 4.1 25.1 - - + +
56A GLY 3.6 6.4 + - - +
57A LYS* 1.3 71.9 - - - +
59A TYR* 1.3 75.5 + - - +
112A TYR* 3.9 34.7 + - + +
114A ILE* 6.4 0.7 - - + -
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Residues in contact with TYR 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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35A PHE* 3.5 30.5 - + + -
51A LEU* 3.2 8.0 - - - +
52A GLY 2.9 34.3 + - - +
54A LYS* 3.9 21.9 + - + -
57A LYS* 3.3 38.3 - - + +
58A LEU* 1.3 84.5 - - - +
60A ALA* 1.3 60.1 + - - +
61A VAL* 4.4 6.5 - - + -
97A TYR* 3.5 41.3 - + - -
98A TYR* 6.2 4.3 - + - -
109A VAL* 3.8 15.3 - - + -
110A MET 3.7 6.7 - - - +
111A GLU* 4.9 0.7 - - - -
112A TYR* 3.9 8.3 - - - -
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Residues in contact with ALA 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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41A ILE* 5.2 1.8 - - + -
49A VAL* 4.2 7.9 - - + -
50A TYR 3.6 4.7 - - - -
51A LEU* 5.0 0.4 - - - +
59A TYR* 1.3 70.5 - - - +
61A VAL* 1.3 60.3 + - - +
62A LYS 3.9 0.4 - - - -
110A MET* 2.9 42.6 + - - +
111A GLU 3.9 5.6 - - - +
112A TYR* 4.0 9.3 - - + +
901A STU 3.3 46.2 - - + +
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Residues in contact with VAL 61 (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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35A PHE* 4.8 12.8 - - + -
49A VAL* 3.5 2.4 - - - +
50A TYR* 2.9 50.5 + - + +
52A GLY* 4.6 11.2 - - - +
59A TYR* 4.4 10.8 - - + +
60A ALA* 1.3 74.3 - - - +
62A LYS* 1.3 61.8 + - - +
63A VAL* 5.1 2.0 - - + -
107A TYR* 4.1 31.6 - - + -
108A LEU 3.0 11.4 - - - +
109A VAL* 4.2 24.2 - - + -
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Residues in contact with LYS 62 (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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48A LYS 3.4 6.3 - - - +
49A VAL* 3.8 21.5 - - + +
60A ALA 3.9 2.0 + - - -
61A VAL* 1.3 72.7 - - - +
63A VAL* 1.3 64.5 + - - +
64A VAL* 4.1 1.5 + - + -
106A VAL 3.9 0.5 - - - +
107A TYR* 3.6 2.6 - - - -
108A LEU* 2.9 47.4 + - + +
110A MET* 3.8 17.0 - - + -
178A SER* 5.6 0.7 - - - +
901A STU 4.7 9.0 - - + -
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Residues in contact with VAL 63 (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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47A GLY 3.2 21.0 + - - +
48A LYS* 2.9 26.2 + - + +
50A TYR* 3.7 33.2 - - + +
61A VAL* 4.7 2.9 - - + +
62A LYS* 1.3 76.1 - - - +
64A VAL* 1.3 64.7 + - - +
105A ASN* 5.8 3.4 - - + -
106A VAL 3.6 4.5 - - - +
107A TYR* 3.5 34.3 - - + -
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Residues in contact with VAL 64 (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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47A GLY 5.0 6.7 - - - +
62A LYS* 5.5 1.8 - - + -
63A VAL* 1.3 79.5 - - - +
65A LYS* 1.3 67.2 + - - +
68A ASP* 6.3 1.1 - - + -
69A MET* 6.0 5.4 - - - +
105A ASN* 3.7 3.0 - - - -
106A VAL* 2.9 56.0 + - + +
108A LEU* 4.5 24.7 - - + -
177A LEU 5.4 3.1 - - - +
178A SER* 5.8 7.2 - - - +
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Residues in contact with LYS 65 (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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64A VAL* 1.3 74.0 - - - +
66A LYS* 1.3 59.4 + - - +
67A ALA* 3.0 17.4 + - + +
68A ASP* 3.2 16.3 + - + +
69A MET* 3.8 7.1 + - - -
104A ASN 4.4 5.6 - - - +
105A ASN* 4.7 2.7 - - - +
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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