Contacts of the strand formed by residues 50 - 58 (chain B) in PDB entry 5D7A
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 LEU 50 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 5.7 2.7 - - + -
41B LYS* 4.1 21.8 - - + +
42B GLY 3.4 15.0 - - - +
43B ARG* 4.7 13.2 - - + +
48B GLY 5.1 3.1 - - - +
49B GLN* 1.3 97.5 - - + +
51B ALA* 1.3 62.6 + - - +
86B TYR* 4.5 4.0 + - - -
107B PHE* 4.2 35.4 + - + +
163B GLU* 6.1 0.4 - - - +
282C GLN* 5.1 0.9 + - - -
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Residues in contact with ALA 51 (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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25B PHE* 3.8 17.9 - - + -
41B LYS 3.8 0.5 - - - -
42B GLY* 2.7 33.9 + - - +
50B LEU* 1.3 79.0 - - - +
52B ALA* 1.3 60.2 + - - +
53B ILE* 4.1 0.9 - - + -
86B TYR* 4.1 9.0 - - + -
104B VAL* 3.8 22.2 - - + -
105B MET 3.7 9.0 - - - +
107B PHE* 3.5 17.0 - - - +
282C GLN* 5.2 0.7 - - - +
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Residues in contact with ALA 52 (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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39B VAL* 4.6 3.8 - - + -
40B TYR 3.5 7.9 - - - +
51B ALA* 1.3 73.2 - - - +
53B ILE* 1.3 60.5 + - - +
103B LEU 3.4 2.1 - - - +
104B VAL* 3.5 0.3 - - - -
105B MET* 2.7 46.3 + - - +
107B PHE* 3.6 10.7 - - + +
401B 58C 3.3 49.1 - - + +
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Residues in contact with ILE 53 (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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25B PHE* 4.2 27.4 - - + -
26B GLU 4.2 8.7 - - - +
27B LEU* 4.3 9.9 - - + -
38B GLN 3.8 0.7 - - - +
39B VAL* 3.2 4.0 - - - -
40B TYR* 2.7 41.4 + - - +
42B GLY* 3.7 26.9 - - - -
51B ALA 4.7 1.1 - - - +
52B ALA* 1.3 78.6 - - - +
54B LYS* 1.3 61.2 + - - +
55B VAL* 3.8 12.1 + - + -
102B TRP* 3.7 42.8 - - + -
103B LEU 3.4 4.5 - - - +
104B VAL* 3.9 18.4 - - + -
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Residues in contact with LYS 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLY* 4.1 7.6 - - - -
35B THR* 2.5 55.7 + - - +
36B TYR 4.5 2.7 - - - -
37B GLY 4.7 1.3 - - - -
38B GLN 3.3 7.9 - - - +
39B VAL* 3.6 19.7 - - + -
52B ALA 4.1 0.4 + - - -
53B ILE* 1.3 73.3 - - - +
55B VAL* 1.3 61.0 + - - +
56B MET* 3.5 32.3 + - + +
69B GLU* 4.6 7.1 + - - -
101B LEU 3.3 3.5 - - - +
103B LEU* 2.9 45.9 + - + +
105B MET* 4.8 9.6 - - + -
171B ASP* 3.3 20.1 + - - +
174B VAL* 4.9 0.2 - - - +
401B 58C 5.0 3.8 - - + -
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 4.4 4.9 - - + -
37B GLY* 3.4 5.4 - - - -
38B GLN* 2.9 35.2 + - - +
40B TYR* 3.6 33.9 - - + -
53B ILE* 4.0 11.9 - - + -
54B LYS* 1.3 75.4 - - - +
56B MET* 1.3 63.3 + - - +
100B GLN* 3.4 40.4 - - + +
101B LEU 3.2 3.6 - - - +
102B TRP* 3.5 25.6 - - + +
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Residues in contact with MET 56 (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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35B THR 4.5 2.5 - - - +
36B TYR* 3.6 24.5 - - - +
37B GLY* 4.7 2.0 - - - -
54B LYS* 3.5 44.2 - - + +
55B VAL* 1.3 81.9 - - - +
57B ASP* 1.3 66.3 + - - +
58B VAL* 3.4 7.4 + - + +
69B GLU* 4.2 14.8 - - - +
100B GLN* 3.5 1.2 - - - -
101B LEU* 2.8 50.1 + - + +
103B LEU* 3.6 27.6 - - + -
174B VAL* 6.1 0.4 - - + -
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Residues in contact with ASP 57 (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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38A GLN* 3.0 34.3 + - - +
55B VAL* 5.4 0.2 - - - +
56B MET* 1.3 71.6 - - - +
58B VAL* 1.3 59.9 + - - +
59B THR* 4.2 2.6 + - - +
62B GLU* 5.3 1.9 - - - +
98B ASP* 3.3 25.9 - - + +
99B ASP 3.5 3.3 - - - +
100B GLN* 3.2 31.9 + - - +
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Residues in contact with VAL 58 (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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15B LEU* 6.0 1.1 - - + -
56B MET* 3.5 19.7 - - + +
57B ASP* 1.3 73.9 - - - +
59B THR* 1.3 77.0 + - - +
60B GLY* 5.4 0.7 - - - -
62B GLU* 5.2 1.8 - - - -
66B ILE* 3.5 35.0 - - + -
90B ILE* 6.1 5.8 - - + -
97B MET 4.8 0.3 - - - +
98B ASP* 3.3 3.8 - - - +
99B ASP* 2.7 56.0 + - + +
101B LEU* 3.7 19.5 - - + +
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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