Contacts of the strand formed by residues 62 - 69 (chain A) in PDB entry 2LA6
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 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A GLU* 3.0 57.9 + - - +
25A VAL* 3.1 43.7 - - + +
53A LEU* 4.1 25.8 - - + -
54A TYR 4.0 5.8 - - - +
55A THR* 3.5 24.2 - - + +
56A ASP* 5.3 0.4 - - - -
61A LYS* 1.3 72.9 - - - +
63A LYS* 1.3 60.6 + - - +
64A GLY 3.5 0.8 + - - +
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Residues in contact with LYS 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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20A GLY* 5.1 2.1 + - - -
22A GLY 5.2 0.2 - - - -
23A GLU* 4.2 9.1 - - - +
54A TYR* 3.0 31.1 + - + +
55A THR 4.1 6.5 - - - +
56A ASP* 3.5 48.0 - - + +
62A LEU* 1.3 71.7 - - - +
64A GLY* 1.3 58.6 + - - +
65A GLU* 3.3 33.2 + - - +
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Residues in contact with GLY 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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19A GLN 3.3 1.7 - - - -
20A GLY* 2.8 25.4 + - - -
21A LEU* 2.8 18.8 + - - +
22A GLY 3.4 31.1 + - - -
25A VAL* 4.5 3.6 - - - +
54A TYR 4.2 0.6 + - - -
62A LEU* 3.3 6.1 + - - +
63A LYS* 1.3 76.4 - - - +
65A GLU* 1.3 65.1 + - - +
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Residues in contact with GLU 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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17A PHE* 3.7 23.1 - - + -
18A VAL 3.2 12.8 - - - +
19A GLN* 3.6 15.6 + - + +
20A GLY 3.2 12.6 + - - -
21A LEU* 3.8 3.2 - - - +
25A VAL* 5.5 1.2 - - - +
53A LEU* 3.6 4.5 - - - +
54A TYR* 2.9 43.4 + - + +
63A LYS* 3.3 42.3 + - - +
64A GLY* 1.3 92.9 - - - +
66A ALA* 1.3 63.3 + - - +
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Residues in contact with ALA 66 (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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16A ILE 3.5 1.7 - - - +
17A PHE* 3.6 2.2 - - - -
18A VAL* 2.9 35.3 + - + +
21A LEU* 3.6 18.2 - - + -
30A VAL* 4.5 6.1 - - + -
51A ILE* 3.8 22.0 - - + -
52A ASN 3.1 13.0 - - - +
53A LEU* 3.8 8.5 - - + -
54A TYR* 3.8 4.2 - - - -
65A GLU* 1.3 76.2 - - - +
67A THR* 1.3 61.5 + - - +
68A VAL* 4.1 1.8 - - + -
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Residues in contact with THR 67 (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 THR* 4.0 13.6 - - - +
16A ILE 3.1 4.5 - - - +
17A PHE* 3.9 13.7 - - + -
50A MET 3.7 2.4 - - - +
51A ILE* 3.1 23.1 - - - -
52A ASN* 3.0 36.2 + - - +
54A TYR* 3.3 28.1 - - + +
66A ALA* 1.3 71.2 - - - +
68A VAL* 1.3 61.0 + - - +
69A SER* 3.9 0.9 + - - -
98A ALA* 4.0 19.5 - - + -
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Residues in contact with VAL 68 (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 THR* 3.3 2.4 - - - -
16A ILE* 2.9 40.6 + - + -
18A VAL* 4.1 21.3 - - + -
30A VAL* 3.5 29.4 - - + -
34A PHE* 4.8 3.1 - - + -
40A ILE* 4.0 18.4 - - + -
50A MET 3.9 2.5 - - - -
51A ILE* 3.9 24.9 - - + -
66A ALA 4.5 2.5 - - - +
67A THR* 1.3 72.2 - - - +
69A SER* 1.3 59.2 + - - +
70A PHE* 3.4 30.3 + - + -
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Residues in contact with SER 69 (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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14A ASN* 3.4 7.2 - - - -
15A THR* 3.0 25.4 + - - +
40A ILE* 3.3 9.1 - - - +
41A LYS* 2.8 46.0 + - - +
50A MET* 3.0 32.9 + - - +
52A ASN* 5.5 3.3 + - - -
67A THR 3.9 1.1 + - - -
68A VAL* 1.3 68.2 - - - +
70A PHE* 1.3 54.2 + - - +
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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