Contacts of the strand formed by residues 53 - 59 (chain N) in PDB entry 4LLG
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 GLU 53 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166I SER* 6.1 0.9 - - - +
20N VAL* 3.6 7.6 - - - +
21N GLU* 3.2 37.5 + - - +
22N SER* 3.2 7.8 + - - -
48N VAL* 5.6 0.4 - - - -
51N GLY 4.2 2.1 + - - +
52N PHE* 1.3 74.4 - - - +
54N VAL* 1.3 62.7 + - - +
55N THR* 3.8 7.2 + - - +
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Residues in contact with VAL 54 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1170J LYS* 5.4 2.0 - - - +
1172J LYS* 3.0 32.7 + - - +
18N ALA* 6.2 1.1 - - + -
19N THR 4.3 3.6 - - - +
20N VAL* 4.3 7.4 - - + -
40N LEU* 5.4 2.9 - - + -
43N ALA* 4.5 7.6 - - + -
44N GLU* 3.7 37.0 - - + +
47N TYR* 4.0 26.0 - - + -
48N VAL* 3.5 22.7 - - + -
52N PHE 3.8 0.4 + - - -
53N GLU* 1.3 74.7 - - - +
55N THR* 1.3 61.5 + - - +
56N ARG 5.8 1.6 - - - +
57N VAL* 6.2 1.8 - - + -
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Residues in contact with THR 55 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1172J LYS* 4.3 9.9 + - - +
1189J MET 4.4 0.5 - - - +
1191J PRO* 3.1 42.9 - - + +
1193J TRP* 5.7 2.2 + - + +
1194J ARG* 5.1 8.7 - - - +
19N THR* 3.0 14.9 + - + -
21N GLU* 3.0 44.4 + - - +
53N GLU* 3.7 8.7 + - - +
54N VAL* 1.3 76.6 - - - +
56N ARG* 1.3 71.5 + - + +
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Residues in contact with ARG 56 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1155J ILE* 3.9 36.5 - - - +
1156J LEU 4.3 13.7 + - - +
1158J GLU* 5.2 0.8 - - - +
1188J GLU* 2.6 41.4 + - - +
1189J MET* 3.2 16.7 + - - +
1190J ILE* 4.3 10.5 - - - +
1191J PRO* 4.5 2.7 - - + -
1219J ASP* 5.8 3.6 + - - -
1222J ARG* 6.1 0.2 - - - +
18N ALA* 3.6 1.0 - - - +
19N THR* 2.9 47.7 + - + +
28N GLU* 4.7 2.6 + - - -
54N VAL* 5.4 1.4 - - - +
55N THR* 1.3 86.8 - - + +
57N VAL* 1.3 78.3 + - - +
58N ARG* 3.8 34.1 - - + +
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Residues in contact with VAL 57 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1188J GLU* 3.5 3.5 - - - +
1189J MET* 2.6 51.9 + - + +
16N PHE* 4.6 4.5 - - + -
17N TRP 3.9 5.6 - - - +
18N ALA* 4.5 12.3 - - + -
36N LEU* 4.4 15.7 - - + +
39N ALA* 4.4 23.1 - - + -
40N LEU* 3.6 36.1 - - + -
43N ALA* 4.9 3.6 - - + -
54N VAL* 6.2 2.0 - - + -
56N ARG* 1.3 82.6 - - - +
58N ARG* 1.3 69.5 + - - +
59N PRO* 4.3 0.2 - - - +
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Residues in contact with ARG 58 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1158J GLU* 3.6 26.0 + - - +
1188J GLU* 4.5 3.8 - - - +
1219J ASP* 5.1 0.4 + - - -
1222J ARG* 3.3 35.9 - - - +
16N PHE* 3.4 8.1 - - - +
17N TRP* 2.9 69.3 + - + +
19N THR* 4.6 1.6 + - - -
28N GLU* 2.7 42.8 + - - -
56N ARG* 3.8 33.1 - - + +
57N VAL* 1.3 75.9 - - - +
59N PRO* 1.3 81.0 + - + +
60N CYS* 5.8 0.2 - - - +
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Residues in contact with PRO 59 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1158J GLU* 3.6 6.6 - - - +
1186J TYR* 4.8 16.4 - - + -
1187J GLU 3.3 31.9 - - - +
1188J GLU* 3.5 18.4 - - + +
16N PHE* 3.5 16.4 - - + -
17N TRP 5.1 0.4 - - - -
36N LEU* 3.7 19.7 - - + -
58N ARG* 1.3 101.8 - - + +
60N CYS* 1.3 64.8 + - - +
61N VAL* 3.4 3.1 + - - +
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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