Contacts of the strand formed by residues 56 - 65 (chain A) in PDB entry 5LPN
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 LYS 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ASP* 3.5 35.8 + - + +
8A LEU* 4.3 21.1 - - + -
52A GLU* 4.4 1.1 - - - -
53A LEU* 2.8 36.6 + - - +
54A GLN 3.4 2.4 + - - +
55A GLY* 1.3 77.5 + - - +
57A LYS* 1.3 59.7 + - - +
58A ILE* 3.8 17.1 + - + +
171A LEU* 4.4 14.1 - - + -
996B GLN* 4.4 7.4 + - - -
1043B GLN* 5.5 4.6 + - - -
1047B LEU* 5.9 3.1 - - - -
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Residues in contact with LYS 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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5A THR* 3.0 33.9 + - - +
6A TYR* 3.3 7.8 - - - +
7A ASP* 2.6 48.4 + - - +
50A THR* 4.6 11.8 - - + +
51A VAL 3.0 13.5 - - - +
52A GLU* 4.0 25.9 + - + +
55A GLY 3.8 4.0 + - - +
56A LYS* 1.3 71.8 - - - +
58A ILE* 1.3 58.3 + - - +
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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 LEU* 3.4 20.6 - - + +
10A PHE* 3.5 43.5 - - + -
50A THR* 3.4 3.7 - - - -
51A VAL* 2.8 44.3 + - + +
53A LEU* 3.5 26.2 - - + -
56A LYS* 4.2 12.6 - - + +
57A LYS* 1.3 76.9 - - - +
59A LYS* 1.3 66.9 + - - +
60A LEU* 4.0 6.1 - - + -
171A LEU* 3.6 33.4 - - + -
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Residues in contact with LYS 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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6A TYR* 3.3 34.6 - - + +
8A LEU 2.8 9.3 + - - -
9A LEU* 3.5 25.1 - - + +
10A PHE 2.9 28.2 + - - +
48A ILE* 3.5 38.6 - - + +
49A LYS 4.1 2.5 - - - -
50A THR* 3.8 16.8 - - - +
58A ILE* 1.3 73.3 - - - +
60A LEU* 1.3 64.0 + - - +
985B VAL* 4.7 5.4 - - + +
988B GLU* 2.5 34.1 + - - +
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Residues in contact with LEU 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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10A PHE* 3.7 14.6 - - + -
12A LEU* 4.2 17.9 - - + -
29A PHE* 4.0 22.2 - - + -
47A LYS 3.6 2.3 - - - +
48A ILE* 3.5 5.7 - - - +
49A LYS 2.9 39.6 + - - +
51A VAL* 3.9 27.8 - - + -
58A ILE* 4.0 17.3 - - + -
59A LYS* 1.3 78.1 - - - +
61A GLN* 1.3 60.0 + - - +
62A ILE* 3.8 16.9 + - + +
163A PHE* 4.9 6.1 - - + +
164A LEU* 5.3 1.1 - - + -
167A ALA* 4.1 22.7 - - + -
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Residues in contact with GLN 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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9A LEU* 4.0 10.5 - - + +
10A PHE 3.0 12.5 + - - +
11A LYS* 3.2 27.1 + - - +
12A LEU 2.9 26.3 + - - +
46A PHE* 3.4 37.7 - - + -
48A ILE* 3.7 13.9 - - + -
59A LYS 3.8 1.6 + - - -
60A LEU* 1.3 69.7 - - - +
62A ILE* 1.3 59.8 + - - +
63A TRP* 3.2 30.3 - - - +
982B ASN* 3.1 21.6 + - - +
985B VAL* 3.7 17.1 - - - +
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Residues in contact with ILE 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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12A LEU* 3.4 24.7 - - + +
14A LEU* 4.0 30.3 - - + -
26A LEU* 3.8 27.5 - - + +
29A PHE* 3.8 26.0 - - + -
46A PHE* 3.0 4.5 - - - -
47A LYS 2.9 35.3 + - - +
49A LYS* 5.5 3.4 - - + +
60A LEU* 3.9 18.2 - - + +
61A GLN* 1.3 74.6 - - - +
63A TRP* 1.3 61.7 + - - +
64A ASP 3.7 1.0 + - - -
163A PHE* 3.6 24.7 - - + -
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Residues in contact with TRP 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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11A LYS* 4.3 13.8 - - + +
12A LEU 2.9 22.0 + - - -
13A LEU* 3.4 23.5 - - + +
14A LEU* 3.0 28.6 + - - +
44A ILE* 3.7 26.0 - - + -
45A ASP 3.1 8.7 - - - +
46A PHE* 3.5 27.8 - + + -
61A GLN* 3.2 45.2 + - - +
62A ILE* 1.3 74.4 - - - +
64A ASP* 1.3 60.7 + - - +
65A THR 3.6 1.3 + - - -
78A TYR* 3.9 29.8 - + + -
978B VAL* 3.9 19.3 - - + -
979B ASP* 6.4 0.7 - - - -
982B ASN* 3.8 22.9 - - + -
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Residues in contact with ASP 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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14A LEU* 4.2 6.6 - - - +
22A LYS* 3.6 23.8 - - - +
23A THR* 2.7 42.4 + - - +
26A LEU* 4.1 18.5 - - + +
41A THR* 3.8 9.2 + - + +
44A ILE* 3.4 5.2 - - - +
45A ASP* 2.8 36.0 + - + +
47A LYS* 6.2 2.0 - - + -
62A ILE 3.7 3.6 + - - -
63A TRP* 1.3 70.3 - - - +
65A THR* 1.3 72.1 + - - +
201A MG 3.6 1.0 - - - -
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Residues in contact with THR 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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13A LEU* 3.5 31.2 - - + -
14A LEU 2.3 33.7 + - - +
15A ILE* 3.6 15.2 - - + +
16A GLY 5.2 0.2 + - - -
22A LYS* 3.6 18.0 - - - -
41A THR* 3.8 10.3 - - - +
43A GLY 3.8 4.9 - - - -
44A ILE* 4.0 12.1 - - + -
64A ASP* 1.3 82.1 + - - +
66A ALA* 1.3 63.4 + - - +
67A GLY 3.9 0.2 + - - -
75A THR* 3.8 20.0 - - + +
79A TYR* 5.2 0.4 - - + -
103A TRP* 6.0 1.0 - - - -
201A MG 4.0 1.0 - - - -
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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