Contacts of the strand formed by residues 52 - 65 (chain B) in PDB entry 5F95
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 GLN 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B VAL* 4.0 5.1 - - - +
42B ALA 2.7 35.1 + - - +
44B PRO* 5.7 1.3 - - + -
50B ARG 3.8 4.9 + - - +
51B PRO* 1.3 74.4 - - - +
53B GLU* 1.3 67.1 + - - +
54B VAL* 3.2 10.8 + - + +
114B TYR* 5.1 8.1 - - + -
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Residues in contact with GLU 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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39B THR* 6.3 2.9 - - - -
40B VAL 3.6 6.3 - - - +
41B VAL* 4.2 19.9 - - + +
52B GLN* 1.3 74.2 - - - +
54B VAL* 1.3 61.7 + - - +
55B SER 4.5 0.2 + - - -
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Residues in contact with VAL 54 (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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38B THR 3.9 0.9 - - - +
39B THR* 3.5 1.9 - - - -
40B VAL* 2.8 42.0 + - + +
42B ALA* 4.2 7.0 - - + -
52B GLN* 3.4 15.7 - - + +
53B GLU* 1.3 75.6 - - - +
55B SER* 1.3 65.1 + - - +
56B TYR* 4.8 7.8 - - + -
75B LEU* 3.9 26.2 - - + -
114B TYR* 3.8 49.4 - - + +
131B VAL* 6.0 1.8 - - + -
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Residues in contact with SER 55 (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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37B VAL* 5.7 3.6 - - - -
38B THR 3.3 8.7 - - - -
39B THR* 4.2 12.6 - - - -
53B GLU 4.5 0.4 + - - -
54B VAL* 1.3 76.8 - - - +
56B TYR* 1.3 64.3 + - - +
75B LEU* 3.6 7.4 - - - +
76B CYS* 2.9 38.3 + - - +
77B ASP* 4.7 1.2 + - - -
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Residues in contact with TYR 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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36B LYS 4.1 0.5 - - - +
37B VAL* 4.5 0.2 - - - -
38B THR* 2.9 73.2 + - + +
40B VAL* 4.7 8.7 - - + +
54B VAL* 4.8 11.2 - - + -
55B SER* 1.3 78.8 - - - +
57B THR* 1.3 57.8 + - - +
59B THR* 4.1 18.2 - - - -
73B ALA* 3.4 21.5 - - + -
74B LYS 3.1 20.6 - - - +
75B LEU* 4.2 9.0 - - + -
76B CYS* 3.9 7.3 - - - -
82B VAL* 6.1 0.4 - - + -
84B ILE* 3.7 29.0 - - + +
116B PHE* 4.2 23.3 - + - -
129B ASN* 5.7 0.5 + - - -
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Residues in contact with THR 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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36B LYS 3.7 22.7 - - - -
37B VAL* 4.6 2.5 - - - -
56B TYR* 1.3 74.4 - - - +
58B ASP* 1.3 82.3 + - - +
59B THR* 2.9 6.1 + - - -
73B ALA* 3.6 4.5 - - - +
74B LYS* 2.8 29.3 + - - -
76B CYS* 4.0 13.1 - - - -
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Residues in contact with ASP 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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36B LYS 4.3 5.1 + - - +
57B THR* 1.3 84.7 - - - +
59B THR* 1.3 65.3 + - - +
60B LYS* 3.3 9.2 + - - +
72B GLN* 3.4 18.2 + - - +
73B ALA* 4.2 0.5 - - - -
74B LYS* 4.2 25.8 - - + +
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Residues in contact with THR 59 (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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36B LYS 5.5 0.8 + - - -
38B THR* 5.5 2.0 - - - -
56B TYR* 4.1 27.4 - - - -
57B THR 2.9 4.1 + - - -
58B ASP* 1.3 77.0 - - - +
60B LYS* 1.3 59.9 + - - +
71B TYR* 5.3 11.0 - - - -
72B GLN 3.2 9.2 - - - -
73B ALA* 4.1 2.2 - - - -
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Residues in contact with LYS 60 (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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58B ASP 3.3 4.7 + - - +
59B THR* 1.3 74.6 - - - +
61B VAL* 1.3 69.6 + - - +
62B ILE* 4.3 10.3 - - + -
71B TYR* 3.2 9.2 - - - -
72B GLN* 2.7 59.5 + - - +
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Residues in contact with VAL 61 (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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60B LYS* 1.3 78.5 - - - +
62B ILE* 1.3 69.4 + - - +
63B GLY 3.6 16.6 - - - +
64B ASN* 5.2 4.5 - - + -
69B VAL* 3.8 14.4 - - + -
70B VAL 3.7 9.2 - - - +
71B TYR* 3.7 24.9 - - + +
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Residues in contact with ILE 62 (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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60B LYS* 4.2 9.4 - - + +
61B VAL* 1.3 79.1 - - - +
63B GLY* 1.3 58.0 + - - +
70B VAL* 2.9 32.1 + - + +
71B TYR 4.0 8.7 - - - +
72B GLN* 3.9 29.2 - - + +
83B ALA* 4.7 2.2 - - + -
134B TYR* 3.9 30.1 - - + +
401B 3UP 4.0 37.1 - - + +
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Residues in contact with GLY 63 (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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61B VAL* 3.6 6.4 - - - +
62B ILE* 1.3 81.5 - - - +
64B ASN* 1.3 60.7 + - - -
67B PHE* 4.6 4.5 - - - -
69B VAL* 3.4 7.6 - - - +
70B VAL* 2.8 35.8 + - - +
401B 3UP 4.7 11.0 - - - -
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Residues in contact with ASN 64 (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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61B VAL* 5.2 4.5 - - + -
63B GLY* 1.3 74.5 - - - +
65B GLY* 1.3 57.5 + - - +
67B PHE* 4.2 5.3 - - - -
68B GLY 3.5 8.7 - - - +
69B VAL* 4.6 11.4 - - + -
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Residues in contact with GLY 65 (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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268A GLU* 4.5 3.4 - - - -
271A LYS* 5.3 2.1 + - - -
64B ASN* 1.3 75.4 - - - +
66B SER* 1.3 66.3 + - - -
67B PHE* 3.1 15.5 - - - -
68B GLY* 2.9 21.7 + - - +
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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