Contacts of the strand formed by residues 8 - 16 (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 LEU 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A TYR* 3.1 9.6 - - - -
7A ASP* 1.3 91.8 - - + +
9A LEU* 1.3 60.7 + - - +
10A PHE* 4.1 19.7 - - + -
56A LYS* 4.3 16.2 - - + -
57A LYS 3.7 2.8 + - - -
58A ILE* 3.4 9.3 - - + +
59A LYS 2.8 25.5 + - - -
171A LEU* 4.2 24.9 - - + -
174A THR* 4.9 5.8 - - + -
993B ILE* 5.0 4.5 - - + -
996B GLN* 5.0 0.4 - - - +
1047B LEU* 4.4 18.6 - - + -
1050B PHE* 3.6 38.8 - - + -
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Residues in contact with LEU 9 (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* 4.2 3.8 - - + +
8A LEU* 1.3 75.2 - - - +
10A PHE* 1.3 72.2 + - - +
11A LYS* 4.2 19.6 + - + +
59A LYS* 3.5 42.2 - - + +
61A GLN* 4.0 26.2 - - + +
83A MET* 3.8 7.4 - - - +
985B VAL* 4.0 20.0 - - + +
986B ALA* 4.9 2.2 - - - -
989B ALA* 3.8 30.7 - - + +
1050B PHE* 4.2 11.5 - - - -
1054B ARG* 4.9 2.8 + - - -
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Residues in contact with PHE 10 (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* 4.1 17.9 - - + -
9A LEU* 1.3 82.4 - - - +
11A LYS* 1.3 65.6 + - - +
12A LEU* 3.8 2.8 + - + +
58A ILE* 3.5 36.6 - - + -
59A LYS 2.9 10.5 + - - +
60A LEU* 3.7 16.4 - - + -
61A GLN* 3.0 28.1 + - - +
83A MET* 3.4 29.4 - - + -
167A ALA* 3.5 27.4 - - - -
170A ILE* 4.0 16.2 - - + -
171A LEU* 3.7 23.6 - - + -
174A THR* 3.8 12.3 - - + -
1050B PHE* 4.4 3.1 - + - -
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Residues in contact with LYS 11 (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* 4.3 18.2 - - + +
10A PHE* 1.3 74.2 - - - +
12A LEU* 1.3 61.7 + - - +
61A GLN* 3.2 29.5 + - - +
63A TRP* 4.3 13.0 - - + +
81A GLY* 3.9 26.9 - - - +
82A ALA* 3.4 7.5 - - + -
83A MET* 2.5 35.6 + - - +
84A GLY 3.1 5.5 + - - -
982B ASN* 3.0 33.3 + - - +
986B ALA* 4.9 9.7 - - - +
1054B ARG* 4.7 7.9 - - - +
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Residues in contact with LEU 12 (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* 4.6 9.4 - - + +
11A LYS* 1.3 76.9 - - - +
13A LEU* 1.3 60.8 + - - +
14A LEU* 5.8 1.3 - - + -
60A LEU* 4.2 27.4 - - + -
61A GLN 2.9 5.5 + - - +
62A ILE* 3.8 31.0 - - + -
63A TRP* 2.9 33.5 + - - -
82A ALA* 4.9 1.3 - - - -
84A GLY* 3.1 18.6 - - - +
86A MET* 6.2 0.2 - - + -
163A PHE* 4.2 19.3 - - + +
166A LEU* 3.7 17.3 - - + -
167A ALA* 5.5 2.0 - - + +
170A ILE* 3.5 31.9 - - + -
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Residues in contact with LEU 13 (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* 1.3 76.9 - - - +
14A LEU* 1.3 65.3 + - - +
15A ILE* 3.8 10.3 - - + -
44A ILE* 4.4 7.0 - - + -
62A ILE* 4.7 0.4 - - - +
63A TRP* 3.4 31.6 - - + +
65A THR* 3.5 23.3 - - + -
78A TYR* 4.9 8.5 - - + +
79A TYR* 3.5 45.8 - - + -
82A ALA* 4.2 10.5 - - + -
84A GLY 2.9 9.2 + - - +
85A ILE* 3.1 19.3 - - + +
86A MET 2.9 25.3 + - - -
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Residues in contact with LEU 14 (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* 5.8 0.2 - - + -
13A LEU* 1.3 76.0 - - - +
15A ILE* 1.3 56.0 - - - +
22A LYS* 3.8 28.1 - - + +
25A VAL* 5.3 4.7 - - + -
26A LEU* 3.9 30.7 - - + +
62A ILE* 4.0 15.5 - - + -
63A TRP 3.0 12.3 + - - +
64A ASP* 4.2 10.3 - - - +
65A THR* 2.3 36.6 + - - +
86A MET* 3.5 36.6 - - + +
88A VAL* 4.8 4.5 - - + -
120A LEU* 5.8 0.7 - - + -
163A PHE* 3.9 19.5 - - + -
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Residues in contact with ILE 15 (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* 3.8 16.4 - - + -
14A LEU* 1.3 78.8 - - - +
16A GLY* 1.3 60.4 + - - +
22A LYS* 3.5 5.2 - - - -
65A THR* 3.6 11.9 - - + +
79A TYR* 3.2 37.0 - - + +
85A ILE* 3.8 6.3 - - + -
86A MET 2.9 14.2 + - - +
87A LEU* 4.0 12.3 - - + -
88A VAL* 2.9 28.1 + - - +
103A TRP* 4.0 24.0 - - + +
107A ILE* 3.6 37.0 - - + -
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Residues in contact with GLY 16 (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 ILE* 1.3 78.7 - - - +
17A ASP* 1.3 62.6 + - - -
20A VAL* 4.7 0.7 - - - -
22A LYS* 2.8 23.1 + - - -
67A GLY* 3.4 5.4 - - - -
88A VAL 3.4 17.3 - - - -
103A TRP* 3.3 29.8 - - - -
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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