Contacts of the strand formed by residues 34 - 42 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A VAL* 4.2 10.3 - - + -
14A TYR 3.5 2.0 - - - -
15A GLN* 3.4 32.8 - - + +
71A LEU* 4.3 3.6 - - - -
83A ALA* 4.8 4.2 - - + +
114A PHE* 4.2 16.8 - - + -
115A PRO* 3.7 18.6 - - + -
116A PRO* 4.0 14.6 - - + -
146A PHE* 5.0 4.5 - - + -
32B HIS* 5.5 0.2 - - + -
33B PHE* 1.3 82.1 - - - +
35B TYR* 1.3 69.3 + - - +
36B GLN* 5.4 2.5 - - + +
58B TYR* 4.0 2.1 - - - -
59B ASN* 2.6 50.0 + - - +
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Residues in contact with TYR 35 (chain B).
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* 3.3 9.4 - - - +
14A TYR* 2.9 33.2 + - + +
67A VAL* 3.2 38.1 - - + -
70A ASN* 3.2 31.7 + - + -
71A LEU* 3.8 30.9 - - + +
74A LEU* 4.4 2.9 - - + -
34B VAL* 1.3 74.8 - - - +
36B GLN* 1.3 79.6 + - - +
37B PHE* 4.7 4.7 - - + -
56B TYR* 3.2 28.7 - + + -
57B ILE 3.6 8.5 - - - -
58B TYR* 4.5 6.5 - + - -
63B TYR* 2.7 43.2 + + - -
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Residues in contact with GLN 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 4.7 1.5 - - + +
12A SER 3.3 3.6 - - - +
13A VAL* 4.2 11.9 - - + -
140A VAL* 3.5 23.3 - - - +
144A TYR* 3.9 21.5 + - - +
146A PHE* 3.3 32.6 - - + -
34B VAL* 5.4 3.0 - - + +
35B TYR* 1.3 82.7 - - - +
37B PHE* 1.3 65.7 + - - +
38B MET* 3.2 29.4 - - - +
55B ARG 3.5 1.7 - - - +
56B TYR* 3.4 4.3 - - - -
57B ILE* 2.8 52.9 + - + +
59B ASN 5.5 2.3 + - - +
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Residues in contact with PHE 37 (chain B).
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 3.5 14.1 - - - -
11A ILE* 3.0 6.1 - - - +
12A SER* 2.6 45.6 + - - +
63A ASN* 3.8 12.1 - - - -
67A VAL* 4.7 4.7 - - + -
6B ALA* 3.7 31.9 - - + -
7B LYS 3.2 21.5 - - - -
8B ALA* 3.9 9.9 - - + -
35B TYR* 4.7 8.2 - - + -
36B GLN* 1.3 75.1 - - - +
38B MET* 1.3 74.0 + - - +
54B THR* 3.9 31.0 - - + -
55B ARG 3.4 9.9 - - - -
56B TYR* 3.8 35.2 - + + -
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Residues in contact with MET 38 (chain B).
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* 4.5 13.5 - - + -
9A TYR 3.8 5.8 - - - -
11A ILE* 4.1 16.2 - - + +
140A VAL* 3.6 25.8 - - + -
141A ASN 5.6 0.2 - - - +
144A TYR* 4.7 11.4 - - + -
36B GLN* 3.2 29.4 - - - +
37B PHE* 1.3 86.7 - - - +
39B GLY* 1.3 60.2 - - - +
40B GLU* 3.3 30.6 + - - +
53B VAL 3.7 0.7 - - - +
54B THR* 3.6 3.5 - - - -
55B ARG* 3.4 33.0 + - + +
57B ILE* 4.4 12.6 - - - -
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Residues in contact with GLY 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLY 3.7 2.6 - - - +
9A TYR* 2.6 39.7 + - - +
6B ALA* 3.7 22.2 - - - +
37B PHE* 4.2 0.4 - - - -
38B MET* 1.3 71.4 - - - +
40B GLU* 1.3 62.2 + - - +
41B CYS* 3.4 2.4 + - - +
52B TYR* 3.6 19.9 - - - -
54B THR* 4.2 5.6 - - - -
104B VAL* 5.8 0.2 - - - +
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Residues in contact with GLU 40 (chain B).
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* 4.9 5.2 - - + -
7A GLY 3.5 9.6 - - - +
8A THR* 4.3 17.2 - - + +
9A TYR 4.5 0.4 - - - +
144A TYR* 6.0 0.2 - - - -
38B MET* 3.3 32.1 + - + +
39B GLY* 1.3 73.8 - - - +
41B CYS* 1.3 58.9 + - - +
42B TYR* 2.0 40.8 + - + +
52B TYR* 3.9 0.2 - - - -
53B VAL* 2.8 43.5 + - + +
55B ARG* 3.1 30.5 + - - -
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Residues in contact with CYS 41 (chain B).
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* 4.9 1.1 - - - +
7A GLY 3.2 22.6 + - - -
9A TYR* 4.2 6.5 - - - -
39B GLY 4.3 0.7 - - - -
40B GLU* 1.3 70.7 - - - +
42B TYR* 1.3 61.4 - - - +
43B PHE* 3.1 25.0 - - - -
51B ARG 3.1 10.8 - - - +
52B TYR* 3.0 27.6 - - + -
104B VAL 4.1 5.2 - - - -
105B CYS* 2.0 51.6 - - - -
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Residues in contact with TYR 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ILE* 3.0 58.9 + - + +
2A GLU 5.1 0.9 - - - +
3A ALA* 3.5 16.6 - - + -
5A HIS 4.1 3.4 - - - -
6A VAL* 4.3 19.3 - - + +
40B GLU* 2.0 56.0 + - + -
41B CYS* 1.3 71.4 - - - +
43B PHE* 1.3 60.7 + - - +
44B THR* 5.0 0.6 - - - +
49B ARG 3.4 2.9 - - - +
50B ILE* 3.1 8.1 - - - -
51B ARG* 2.7 58.5 + - + +
53B VAL* 4.2 13.0 - - + -
55B ARG* 4.2 0.7 + - - -
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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