Contacts of the strand formed by residues 34 - 42 (chain F) 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 34 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13E VAL* 4.1 23.1 - - + -
14E TYR 3.4 2.9 - - - +
15E GLN* 3.4 31.4 - - + +
71E LEU* 4.1 5.6 - - - +
83E ALA* 4.9 4.6 - - + +
114E PHE* 4.3 14.4 - - + -
115E PRO* 3.8 15.9 - - + -
116E PRO* 4.0 11.0 - - + -
146E PHE* 4.8 5.2 - - + -
32F HIS* 5.3 0.4 - - + -
33F PHE* 1.3 77.0 - - - +
35F TYR* 1.3 64.5 + - - +
36F GLN* 5.4 2.0 - - + +
57F ILE 3.9 0.2 - - - +
58F TYR* 3.7 0.9 - - - -
59F ASN* 2.7 54.7 + - - +
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Residues in contact with TYR 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E SER 4.2 0.2 - - - -
13E VAL* 3.2 9.9 - - - +
14E TYR 2.8 32.2 + - - +
67E VAL* 3.1 39.9 - - + -
70E ASN* 3.7 21.3 + - + -
71E LEU* 3.8 32.7 - - + +
74E LEU* 4.1 9.2 - - + -
34F VAL* 1.3 75.4 - - - +
36F GLN* 1.3 79.4 + - - +
37F PHE* 4.7 4.3 - - + -
56F TYR* 3.2 22.6 - + + +
57F ILE 3.6 11.4 - - - -
58F TYR* 4.5 6.3 - + - -
59F ASN 5.9 0.2 - - - -
63F TYR* 2.4 51.5 + + - -
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Residues in contact with GLN 36 (chain F).
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* 5.2 1.8 - - + -
12E SER 3.3 4.7 - - - +
13E VAL* 4.3 10.1 - - + -
114E PHE* 6.0 0.4 - - - -
140E VAL* 3.5 14.6 - - - +
144E TYR* 3.8 31.3 + - - +
146E PHE* 3.3 31.5 - - + -
34F VAL* 5.4 3.5 - - + +
35F TYR* 1.3 82.1 - - - +
37F PHE* 1.3 67.6 + - - +
38F MET* 3.0 28.7 - - - +
55F ARG 3.6 1.4 - - - +
56F TYR* 3.4 3.8 - - - -
57F ILE* 2.8 53.8 + - + +
59F ASN 5.7 1.9 + - - +
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Residues in contact with PHE 37 (chain F).
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 3.6 6.7 - - - -
11E ILE* 3.0 5.9 - - - +
12E SER* 2.6 43.5 + - - +
63E ASN* 3.5 18.8 - - - -
67E VAL* 4.4 9.0 - - + -
6F ALA* 3.6 27.8 - - + -
7F LYS 3.1 27.8 - - - -
8F ALA* 3.7 7.0 - - + -
35F TYR* 4.6 3.3 - - + -
36F GLN* 1.3 75.5 - - - +
38F MET* 1.3 70.7 + - - +
54F THR* 3.8 24.7 - - + -
55F ARG 3.4 11.7 - - - -
56F TYR* 3.1 48.7 - + + -
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Residues in contact with MET 38 (chain F).
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* 3.7 19.3 - - + -
9E TYR 3.6 5.8 - - - -
10E GLY 4.2 1.3 - - - -
11E ILE* 4.0 16.6 - - + +
140E VAL* 4.1 18.2 - - + -
144E TYR* 4.6 12.8 - - + -
36F GLN* 3.0 29.8 - - + +
37F PHE* 1.3 85.6 - - - +
39F GLY* 1.3 59.4 + - - +
40F GLU* 2.6 38.4 + - + +
53F VAL 3.7 0.7 - - - +
54F THR* 3.6 3.5 - - - -
55F ARG* 3.4 38.3 + - + +
57F ILE* 4.8 0.9 - - + -
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Residues in contact with GLY 39 (chain F).
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 3.6 5.4 - - - +
9E TYR* 2.5 36.4 + - - +
6F ALA* 3.7 21.9 - - - +
37F PHE* 4.4 0.2 - - - -
38F MET* 1.3 70.1 - - - +
40F GLU* 1.3 63.1 + - - -
41F CYS* 3.4 3.1 + - - -
52F TYR* 3.6 20.5 - - - -
53F VAL 4.2 0.2 - - - -
54F THR* 4.2 4.5 - - - -
104F VAL* 5.8 0.2 - - - +
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Residues in contact with GLU 40 (chain F).
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* 4.9 5.6 - - + -
7E GLY 3.3 8.7 - - - +
8E THR* 3.9 17.8 - - + +
9E TYR 4.4 0.8 - - - +
144E TYR* 5.9 0.2 - - - -
38F MET* 2.6 36.1 + - + +
39F GLY* 1.3 74.4 - - - +
41F CYS* 1.3 59.0 + - - +
42F TYR* 2.4 39.4 + - + +
52F TYR* 4.0 0.2 - - - -
53F VAL* 2.9 50.1 + - - +
55F ARG* 2.8 31.6 + - - +
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Residues in contact with CYS 41 (chain F).
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* 5.1 0.9 - - - +
7E GLY 3.0 14.6 + - - -
9E TYR* 3.9 15.7 - - - -
39F GLY 4.1 4.3 - - - -
40F GLU* 1.3 72.1 - - - +
42F TYR* 1.3 59.3 + - - +
43F PHE* 3.0 34.8 - - - -
51F ARG 3.1 10.1 - - - +
52F TYR* 3.2 25.8 - - + -
104F VAL 3.9 3.8 - - - -
105F CYS* 2.0 51.8 - - + -
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Residues in contact with TYR 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E ILE* 2.9 55.8 + - + -
2E GLU 5.1 0.9 - - - +
3E ALA* 3.6 15.9 - - + -
5E HIS 4.0 3.8 - - - -
6E VAL* 4.7 17.7 - - + +
40F GLU* 2.4 52.9 + - + -
41F CYS* 1.3 72.5 - - - +
43F PHE* 1.3 61.2 + - - +
49F ARG 3.4 2.6 - - - +
50F ILE* 3.1 7.6 - - - -
51F ARG* 2.6 58.3 + - + +
53F VAL* 4.4 12.6 - - + -
55F ARG* 3.8 7.5 + - - -
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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