Contacts of the strand formed by residues 6 - 15 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E ALA* 5.6 1.8 - - + +
4E ASP 5.0 4.0 - - - +
5E HIS* 1.3 75.9 - - - +
7E GLY* 1.3 69.0 + - - +
8E THR* 3.8 10.7 + - + +
27E PHE* 3.0 18.6 - - - -
28E ASP* 3.2 30.3 + - - +
29E GLY 5.2 1.1 - - - +
40F GLU* 4.9 7.2 - - + -
41F CYS 4.4 4.5 - - - +
42F TYR* 4.7 29.4 - - + +
43F PHE* 4.3 0.7 - - - +
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Residues in contact with GLY 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E VAL* 1.3 75.0 - - - +
8E THR* 1.3 61.1 + - - -
9E TYR* 3.4 33.0 - - - -
27E PHE* 3.6 6.5 - - - -
39F GLY 3.6 2.9 - - - +
40F GLU* 3.3 1.6 - - - -
41F CYS 3.0 34.4 + - - -
43F PHE* 3.5 6.5 - - - -
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Residues in contact with THR 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E VAL* 4.4 12.6 + - + +
7E GLY* 1.3 70.8 - - - -
9E TYR* 1.3 65.0 + - - +
11E ILE* 3.9 17.0 - - + -
25E PHE* 3.5 0.2 - - - -
26E GLU* 2.6 64.9 + - - +
27E PHE* 4.6 0.7 + - - -
28E ASP 5.2 1.0 + - - -
29E GLY 5.6 1.2 + - - -
140E VAL* 5.2 3.6 - - + -
38F MET* 3.7 31.6 - - + -
40F GLU* 3.9 13.7 - - + +
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Residues in contact with TYR 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E GLY* 3.4 29.1 - - - -
8E THR* 1.3 90.9 - - - +
10E GLY* 1.3 60.6 + - - +
11E ILE* 2.9 7.8 + - - -
25E PHE* 3.2 34.8 - + + +
26E GLU 3.8 6.1 - - - -
27E PHE* 4.1 0.7 - - - -
32E LEU* 3.7 22.2 - - + -
4F GLN 4.8 2.5 - - - +
6F ALA* 4.6 7.6 - - + +
38F MET* 3.5 1.0 - - - -
39F GLY* 2.5 48.0 + - - +
41F CYS* 3.9 17.0 - - - -
43F PHE* 4.2 8.5 - + - -
104F VAL* 4.2 8.1 - - + -
105F CYS* 4.8 0.2 - - - -
108F ASN* 3.9 29.2 - - + +
109F TYR 5.1 0.2 + - - -
113F GLU* 3.3 24.8 + - - +
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Residues in contact with GLY 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E TYR* 1.3 74.3 - - - +
11E ILE* 1.3 56.5 + - - +
12E SER* 2.6 25.9 + - - -
23E TYR* 2.9 29.8 - - - -
25E PHE* 3.5 15.0 - - - -
63E ASN* 3.7 0.5 + - - -
6F ALA* 4.4 12.1 - - - -
37F PHE* 3.4 14.8 - - - +
38F MET* 4.4 0.4 - - - -
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Residues in contact with ILE 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E THR* 3.9 13.5 - - + -
9E TYR 2.9 11.6 + - - +
10E GLY* 1.3 74.1 - - - +
12E SER* 1.3 59.4 + - - +
13E VAL* 4.1 15.9 - - + -
22E GLN* 3.5 3.1 - - - +
23E TYR* 3.3 6.2 - - - -
24E THR* 2.8 62.1 + - + +
26E GLU* 3.8 27.4 - - + +
140E VAL* 3.8 34.1 - - + -
146E PHE* 5.7 0.4 - - + -
36F GLN* 5.1 3.8 - - + +
37F PHE 3.0 11.4 - - - +
38F MET* 4.0 11.7 - - + +
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Residues in contact with SER 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E GLY 2.6 12.5 + - - -
11E ILE* 1.3 69.6 - - - +
13E VAL* 1.3 62.0 + - - +
22E GLN 3.6 3.8 - - - -
23E TYR* 3.1 16.0 - - - -
63E ASN* 2.4 26.6 + - - -
64E ILE* 4.3 4.9 - - - -
67E VAL* 3.2 32.1 - - - +
35F TYR 3.6 0.5 - - - +
36F GLN* 3.3 4.7 - - - -
37F PHE* 2.6 37.5 + - - -
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Residues in contact with VAL 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ILE* 4.6 11.0 - - + -
12E SER* 1.3 79.9 - - - +
14E TYR* 1.3 68.4 + - - +
15E GLN* 5.1 2.0 - - + +
20E ILE 4.4 0.9 - - - +
21E GLY* 3.3 3.8 - - - -
22E GLN* 3.0 50.3 + - + +
64E ILE* 4.1 3.9 - - - +
67E VAL* 4.4 0.4 - - - -
116E PRO* 4.3 16.6 - - + -
146E PHE* 4.0 26.7 - - + -
34F VAL* 4.1 17.9 - - + -
35F TYR 3.2 11.2 - - - +
36F GLN* 4.3 10.1 - - + -
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Residues in contact with TYR 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E VAL* 1.3 77.5 - - - +
15E GLN* 1.3 77.4 + - - +
16E SER* 4.5 3.8 + - - -
19E ASP* 2.5 57.8 + - - +
20E ILE 3.1 16.8 - - - -
21E GLY* 3.9 6.7 - - - -
64E ILE* 4.0 17.3 - - + -
67E VAL* 3.7 22.4 - - + +
68E LYS* 3.1 47.2 - - + +
71E LEU* 3.8 18.2 - - + +
33F PHE 3.8 0.3 - - - +
34F VAL* 3.4 4.0 - - - +
35F TYR* 2.8 31.8 + - + +
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Residues in contact with GLN 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E VAL* 5.1 2.0 - - + +
14E TYR* 1.3 78.9 - - - +
16E SER* 1.3 68.4 + - - +
17E PRO* 3.5 7.0 - - + +
19E ASP* 3.3 4.2 + - - -
20E ILE* 2.8 51.7 + - + +
71E LEU* 4.0 1.8 - - - -
115E PRO* 3.2 33.1 - - - +
116E PRO* 3.2 34.5 - - + +
117E VAL* 3.4 21.8 - - - +
169E TRP* 5.0 2.0 - - - -
32F HIS* 5.4 3.4 - - + +
33F PHE 3.0 4.7 - - - +
34F VAL* 3.4 22.8 - - + +
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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