Contacts of the strand formed by residues 6 - 15 (chain A) in PDB entry 1LNU
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 VAL 6 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ALA* 5.6 1.3 - - + +
4A ASP 3.8 2.0 + - - +
5A HIS* 1.3 76.2 - - - +
7A GLY* 1.3 65.1 + - - +
8A THR* 3.8 15.9 + - - +
27A PHE* 3.1 16.9 - - - -
28A ASP* 3.1 32.3 + - - +
29A GLY 5.2 1.8 - - - +
40B GLU* 4.9 6.5 - - + -
41B CYS 4.4 4.0 - - - +
42B TYR* 4.3 33.0 - - + -
43B PHE* 4.3 1.6 - - - +
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Residues in contact with GLY 7 (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 VAL* 1.3 74.3 - - - +
8A THR* 1.3 59.4 + - - -
9A TYR* 3.2 42.7 - - - -
27A PHE* 3.5 6.3 - - - -
40B GLU* 3.5 0.9 - - - -
41B CYS 3.2 33.0 + - - +
43B PHE* 3.6 6.3 - - - -
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Residues in contact with THR 8 (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 VAL* 4.2 17.3 + - - +
7A GLY* 1.3 70.3 - - - -
9A TYR* 1.3 64.6 + - - +
11A ILE* 3.1 33.9 - - + -
25A PHE* 3.5 0.3 - - - -
26A GLU* 2.6 60.1 + - + +
27A PHE* 5.2 0.5 - - - -
28A ASP 5.4 0.5 + - - -
140A VAL* 5.0 4.5 - - + -
38B MET* 4.5 20.2 - - + -
40B GLU* 4.3 13.1 - - + +
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Residues in contact with TYR 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLY* 3.2 41.0 - - - -
8A THR* 1.3 89.0 - - - +
10A GLY* 1.3 63.4 + - - +
11A ILE* 3.0 4.8 + - - +
25A PHE* 3.0 37.5 - + + +
26A GLU 3.8 2.9 - - - -
27A PHE* 3.4 5.5 - - - -
32A LEU* 3.8 14.6 - - + -
4B GLN 4.8 3.6 - - - +
6B ALA* 4.6 7.6 - - + -
38B MET* 3.6 0.9 - - - -
39B GLY* 2.6 46.4 + - - +
41B CYS* 4.2 14.6 - - - -
43B PHE* 4.6 5.9 - + - -
104B VAL* 4.5 6.1 - - + -
108B ASN* 4.1 26.9 - - + +
113B GLU* 2.6 33.0 + - - +
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Residues in contact with GLY 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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9A TYR* 1.3 74.1 - - - +
11A ILE* 1.3 66.4 + - - +
12A SER* 2.9 13.9 + - - -
23A TYR* 3.2 30.0 - - - -
25A PHE* 3.3 13.5 - - - -
63A ASN* 4.0 0.5 + - - -
6B ALA* 4.4 13.9 - - - -
37B PHE* 3.4 16.4 - - - +
38B MET* 4.4 0.7 - - - -
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Residues in contact with ILE 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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8A THR* 3.1 40.8 - - + +
9A TYR 3.0 7.4 + - - +
10A GLY* 1.3 75.3 - - - +
12A SER* 1.3 58.8 + - - +
13A VAL* 4.6 14.8 - - + -
22A GLN* 3.5 3.8 - - - +
23A TYR* 3.3 6.2 - - - -
24A THR* 2.9 59.6 + - + +
26A GLU* 4.0 15.0 - - + +
140A VAL* 3.7 29.6 - - + -
146A PHE* 5.7 0.2 - - + -
36B GLN* 4.7 3.6 - - - +
37B PHE 3.0 10.5 - - - +
38B MET* 4.1 8.1 - - + -
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Residues in contact with SER 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 GLY 2.9 3.8 + - - -
11A ILE* 1.3 71.4 - - - +
13A VAL* 1.3 62.2 + - - +
22A GLN 3.7 3.8 - - - -
23A TYR* 3.1 20.2 - - - -
63A ASN* 2.9 27.3 + - - +
64A ILE* 4.6 3.4 - - - -
67A VAL* 3.1 31.0 - - - +
35B TYR 3.7 0.7 - - - +
36B GLN* 3.3 4.2 - - - -
37B PHE* 2.6 39.5 + - - -
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Residues in contact with VAL 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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11A ILE* 4.6 10.1 - - + -
12A SER* 1.3 79.9 - - - +
14A TYR* 1.3 68.3 + - - +
15A GLN* 5.0 2.9 - - - +
20A ILE 4.4 0.9 - - - +
21A GLY* 3.3 3.3 - - - -
22A GLN* 3.0 50.8 + - + +
64A ILE* 3.9 4.0 - - - +
67A VAL* 4.3 0.4 - - - -
116A PRO* 4.3 16.2 - - + -
146A PHE* 3.8 28.7 - - + -
34B VAL* 4.2 17.0 - - + -
35B TYR 3.3 11.2 - - - +
36B GLN* 4.2 10.8 - - + -
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Residues in contact with TYR 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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13A VAL* 1.3 76.8 - - - +
15A GLN* 1.3 72.0 + - - +
16A SER* 4.6 4.0 + - - -
19A ASP* 2.5 56.4 + - - +
20A ILE 3.1 14.6 - - - -
21A GLY* 4.0 2.5 - - - -
64A ILE* 3.9 23.1 - - + -
67A VAL* 3.5 22.4 - - + +
68A LYS* 2.9 49.8 - - + +
71A LEU* 4.0 17.1 - - + +
34B VAL* 3.5 2.3 - - - +
35B TYR* 2.9 31.9 + - + +
51C GLN* 5.9 1.4 - - - +
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Residues in contact with GLN 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 VAL* 5.0 2.5 - - + +
14A TYR* 1.3 79.7 - - - +
16A SER* 1.3 69.3 + - - +
17A PRO* 3.5 6.6 - - + +
19A ASP* 3.3 17.3 + - - -
20A ILE* 2.8 41.3 + - + +
71A LEU* 4.0 1.1 - - - -
115A PRO* 3.3 25.5 - - - +
116A PRO* 3.2 32.2 - - + +
117A VAL* 3.0 29.2 - - - +
169A TRP* 5.1 1.0 - - - -
32B HIS* 5.4 3.6 - - - +
33B PHE 3.0 4.3 - - - +
34B VAL* 3.4 23.7 - - + +
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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