Contacts of the strand formed by residues 97 - 108 (chain A) in PDB entry 4LCC
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 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A PHE* 3.8 24.9 - - + -
35A TYR* 5.2 2.5 - - + +
89A ALA* 4.0 8.3 - - + -
90A VAL 3.7 8.5 - - - +
91A LYS* 3.4 43.5 - - + +
95A TYR 3.6 1.7 + - - +
96A GLN* 1.3 78.9 - - - +
98A ILE* 1.3 62.1 + - - +
99A TRP* 3.6 45.5 + - + +
35B TYR* 4.9 7.6 - - - +
45B LEU* 6.1 0.9 - - - +
104B LEU* 4.6 14.4 - - + -
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Residues in contact with ILE 98 (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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2A GLN 3.8 20.6 - - - +
3A ASN* 5.3 0.4 - - - +
4A ILE* 4.1 20.8 - - + +
26A THR* 3.8 20.9 - - + -
89A ALA* 3.3 2.6 - - - -
90A VAL* 3.0 39.5 + - + +
92A ASP* 3.2 31.2 - - + +
96A GLN* 3.4 25.4 - - - +
97A LEU* 1.3 73.7 - - - +
99A TRP* 1.3 63.7 + - - +
100A GLY 3.9 0.5 + - - -
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Residues in contact with TRP 99 (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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4A ILE* 3.7 7.4 - - - +
35A TYR* 3.2 42.6 - + + -
87A LEU* 3.7 34.1 - - + -
88A CYS 3.8 4.5 - - - -
89A ALA* 3.4 17.5 - - + -
97A LEU* 3.6 40.6 - - + +
98A ILE* 1.3 75.4 - - - +
100A GLY* 1.3 62.9 + - - +
101A ALA 4.1 0.3 + - - -
35B TYR* 3.9 21.4 + + - -
42B GLY* 4.3 6.6 + - - -
43B LEU* 3.7 52.1 + - + +
104B LEU* 4.2 4.5 - - + -
106B PHE* 3.9 24.7 - + - -
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Residues in contact with GLY 100 (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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4A ILE* 3.5 28.1 - - - +
6A GLN* 3.3 11.6 - - - +
87A LEU* 4.5 5.5 - - - +
88A CYS 2.6 25.1 + - - +
99A TRP* 1.3 78.3 - - - +
101A ALA* 1.3 67.0 + - - -
102A GLY* 3.3 2.6 + - - -
42B GLY* 4.2 5.4 - - - -
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Residues in contact with ALA 101 (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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4A ILE 5.1 1.4 + - - -
6A GLN* 2.9 23.7 - - - +
99A TRP 4.1 0.2 + - - -
100A GLY* 1.3 69.2 - - - -
102A GLY* 1.3 67.9 + - - +
40B GLY* 4.1 9.2 - - - +
41B MET* 3.8 13.9 - - - +
42B GLY* 3.6 27.6 - - - +
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Residues in contact with GLY 102 (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 GLN* 3.4 4.0 - - - -
7A PRO 3.6 5.0 - - - +
8A THR* 3.9 9.4 - - - +
85A SER* 4.9 4.9 - - - -
86A TYR 3.1 15.7 - - - -
87A LEU* 3.7 22.9 - - - +
100A GLY 3.3 3.0 + - - -
101A ALA* 1.3 79.8 - - - +
103A THR* 1.3 61.9 + - - -
104A LYS 3.9 2.2 + - - -
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Residues in contact with THR 103 (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 GLN* 3.2 16.8 + - - +
7A PRO* 2.6 41.8 + - + +
10A MET* 4.2 18.6 - - + +
20A ILE* 3.3 36.3 - - + +
84A ALA 3.4 2.8 - - - +
85A SER* 4.0 0.9 - - - -
86A TYR* 2.8 35.5 + - - -
102A GLY* 1.3 71.1 - - - -
104A LYS* 1.3 69.6 + - - +
105A LEU* 3.4 0.9 + - - -
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Residues in contact with LYS 104 (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 THR 3.0 17.5 + - - +
9A GLU* 3.2 14.3 - - + +
10A MET 2.9 27.9 + - - +
84A ALA 3.6 6.1 - - - -
85A SER* 3.7 17.0 + - - +
102A GLY 3.9 1.8 + - - -
103A THR* 1.3 70.3 - - - +
105A LEU* 1.3 60.8 + - - +
106A ILE* 4.0 4.0 - - + -
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Residues in contact with LEU 105 (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 MET* 3.5 23.3 - - + +
12A ALA* 4.8 5.6 - - + +
18A VAL* 4.0 41.1 - - + -
20A ILE* 5.1 8.7 - - + -
75A LEU* 4.1 15.7 - - + -
78A LEU* 4.5 1.6 - - + -
82A ASP 3.8 12.6 - - - +
83A SER* 3.2 22.3 - - - -
84A ALA 2.8 20.6 + - - +
86A TYR* 3.9 11.2 - - + -
103A THR 3.4 1.5 + - - +
104A LYS* 1.3 72.6 - - - +
106A ILE* 1.3 63.1 + - - +
107A ILE* 3.6 28.0 - - + -
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Residues in contact with ILE 106 (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 GLU* 3.1 44.2 - - + +
10A MET 2.9 10.6 + - - +
11A THR* 3.5 16.7 - - + +
12A ALA 3.2 23.0 + - - -
83A SER* 4.4 1.6 - - - -
104A LYS* 4.5 5.2 - - + +
105A LEU* 1.3 76.0 - - - +
107A ILE* 1.3 67.5 + - - +
108A LYS* 3.6 1.5 + - - -
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Residues in contact with ILE 107 (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 ALA 3.2 3.4 - - - +
13A THR 4.4 0.4 - - - -
14A GLU* 3.8 25.4 - - - +
78A LEU* 3.7 25.8 - - + -
79A GLN 3.5 24.9 - - - +
80A MET* 3.7 24.8 - - + +
82A ASP* 4.2 0.9 - - + -
83A SER* 3.5 34.5 - - - +
105A LEU* 3.6 32.8 - - + -
106A ILE* 1.3 76.3 - - - +
108A LYS* 1.3 63.4 + - - +
109A PRO* 3.6 6.9 - - - +
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Residues in contact with LYS 108 (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 THR* 4.9 11.0 - - + -
12A ALA 2.7 11.8 + - - +
13A THR* 3.1 27.8 - - + +
14A GLU* 2.4 32.6 + - - -
106A ILE* 3.6 2.0 + - - -
107A ILE* 1.3 70.3 - - - +
109A PRO* 1.3 69.1 - - + +
156A LYS* 5.4 8.7 - - - +
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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