Contacts of the strand formed by residues 20 - 27 (chain G) 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 ILE 20 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G VAL* 4.4 0.9 - - - +
14G TYR* 3.1 7.8 - - - -
15G GLN* 2.8 53.8 + - + +
17G PRO 3.7 18.8 - - - +
18G GLY* 3.1 18.2 - - - +
19G ASP* 1.3 75.3 - - - +
21G GLY* 1.3 64.7 + - - +
116G PRO 5.1 3.8 - - - +
117G VAL* 4.2 24.2 - - + -
169G TRP* 5.9 1.6 - - + -
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Residues in contact with GLY 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G VAL* 3.3 8.7 - - - -
14G TYR* 3.9 9.8 - - - -
19G ASP 3.7 4.2 + - - -
20G ILE* 1.3 81.4 - - - +
22G GLN* 1.3 62.8 + - - +
37G LEU* 3.4 26.3 - - - +
64G ILE* 5.0 1.6 - - - -
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Residues in contact with GLN 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G ILE 3.5 2.8 - - - +
12G SER* 3.7 1.2 - - - -
13G VAL* 3.0 48.1 + - + +
21G GLY* 1.3 73.9 - - - +
23G TYR* 1.3 60.1 + - - +
24G THR* 3.5 22.0 + - + +
34G TYR* 5.6 2.5 - - + -
35G VAL 5.8 0.2 - - - -
37G LEU* 3.9 3.9 - - - +
64G ILE* 4.0 4.3 - - - +
137G SER* 3.6 14.4 + - - +
138G PHE* 3.2 67.0 + - + +
146G PHE* 5.1 5.5 - - - -
148G LYS* 5.2 0.2 + - - -
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Residues in contact with TYR 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G GLY* 3.0 30.0 - - - -
11G ILE 3.3 2.2 - - - -
12G SER* 3.2 28.7 - - - -
22G GLN* 1.3 75.8 - - - +
24G THR* 1.3 65.7 + - - +
25G PHE* 3.1 21.4 - + - -
33G PHE* 5.0 0.4 - + - -
34G TYR* 3.4 1.1 - - - +
35G VAL* 3.1 56.5 + - + -
37G LEU* 4.4 7.2 - - + +
55G PHE* 3.6 23.1 - + - -
59G GLY 4.7 0.4 - - - -
60G GLY* 3.5 26.0 - - - +
63G ASN* 3.8 14.6 - - + -
64G ILE* 4.0 10.3 - - + -
5H LYS* 3.3 20.1 - - - +
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Residues in contact with THR 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G ILE* 2.8 68.8 + - - +
22G GLN* 3.5 35.9 + - + +
23G TYR* 1.3 82.6 - - - +
25G PHE* 1.3 69.4 + - - +
26G GLU* 4.1 6.7 + - - +
31G GLU* 5.0 4.5 - - - -
33G PHE* 3.8 9.0 - - - -
34G TYR* 4.0 13.2 - - + -
137G SER* 4.0 8.5 - - - -
138G PHE 4.8 2.4 + - - +
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Residues in contact with PHE 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G THR 3.6 3.1 - - - -
9G TYR* 3.0 31.0 - + + -
10G GLY 3.0 26.0 - - - -
23G TYR* 3.1 27.8 - + - -
24G THR* 1.3 76.0 - - - +
26G GLU* 1.3 62.7 + - - +
31G GLU* 3.7 4.2 - - - +
32G LEU* 2.9 33.5 + - + +
33G PHE* 3.3 39.3 + + + +
55G PHE* 3.6 17.5 - + - -
3H ALA* 4.1 12.3 - - + -
4H GLN 3.4 26.2 - - - -
5H LYS* 3.7 5.2 - - - -
108H ASN* 3.9 5.6 - - - -
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Residues in contact with GLU 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G GLY* 3.9 1.2 - - - -
8G THR* 2.6 55.1 + - - +
9G TYR* 4.0 4.3 - - - -
11G ILE* 3.1 14.7 - - + +
24G THR* 4.1 7.8 + - - +
25G PHE* 1.3 78.8 - - - +
27G PHE* 1.3 64.3 + - - +
29G GLY* 4.6 11.7 - - - +
30G ASP 3.3 11.0 - - - +
31G GLU* 4.4 9.4 - - + +
32G LEU* 4.2 2.5 - - - -
138G PHE 4.2 2.5 - - - +
139G PHE* 4.0 21.2 - - + -
140G VAL* 2.9 44.8 + - - +
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Residues in contact with PHE 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G HIS* 3.8 16.6 - - + -
6G VAL 2.9 39.9 - - - -
7G GLY* 3.6 10.8 - - - -
8G THR* 5.2 0.2 - - - -
9G TYR* 3.9 6.5 - - - -
26G GLU* 1.3 75.2 - - - +
28G ASP* 1.3 85.6 + - + +
29G GLY 3.2 0.9 - - - -
30G ASP* 2.6 39.9 + - - +
32G LEU* 3.9 18.2 - - + -
43H PHE* 4.3 5.4 - + - -
109H TYR* 5.3 1.8 - + - -
113H GLU* 3.9 14.4 - - + -
117H SER* 2.8 39.5 - - - +
118H LEU* 3.6 18.2 - - + -
150H TYR* 5.1 2.5 - - - -
180H TRP* 4.2 6.8 - + + -
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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