Contacts of the strand formed by residues 56 - 61 (chain B) in PDB entry 4M6W
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 CYS 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B TYR* 3.7 1.6 - - - -
52B LEU* 3.1 45.7 + - + -
53B SER* 3.2 25.6 + - - +
54B ASN 3.9 0.2 - - - -
55B ARG* 1.3 81.9 - - + +
57B CYS* 1.3 65.9 + - - +
85B LEU* 4.0 2.6 - - - +
86B LYS* 3.3 33.7 - - + +
88B ILE* 4.4 9.9 - - - -
136B GLN* 3.9 11.7 - - - +
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Residues in contact with CYS 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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48B PRO* 3.8 25.6 - - + -
50B PHE 3.4 14.1 - - - +
51B TYR* 4.0 5.2 - - + -
52B LEU* 4.2 4.3 - - - +
56B CYS* 1.3 80.0 - - - +
58B ILE* 1.3 65.1 + - - +
59B LEU* 4.8 2.0 - - - -
79B VAL* 4.1 7.6 - - - -
85B LEU* 3.8 26.7 - - + -
86B LYS 3.0 7.1 + - - +
87B GLY* 3.6 17.4 - - - -
88B ILE* 2.9 31.3 + - - +
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Residues in contact with ILE 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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48B PRO* 3.5 2.3 - - - +
49B ASP* 3.0 23.7 + - - -
50B PHE* 2.8 41.8 + - + +
52B LEU* 3.7 28.0 - - + +
57B CYS* 1.3 74.9 - - - +
59B LEU* 1.3 69.3 + - - +
60B TYR* 4.4 3.4 - - + +
88B ILE* 3.4 21.1 - - + +
90B VAL* 3.9 23.3 - - + -
129B VAL* 3.9 30.1 - - + -
132B LEU* 3.9 16.2 - - + -
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Residues in contact with LEU 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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47B THR 4.3 0.9 - - - +
48B PRO* 4.1 13.0 - - + -
49B ASP* 3.9 3.1 - - - -
57B CYS* 4.8 1.1 - - - -
58B ILE* 1.3 77.1 - - - +
60B TYR* 1.3 61.3 - - - +
61B VAL* 5.6 0.4 - - + -
75B ARG* 3.4 34.8 - - + +
76B LEU* 3.8 34.5 - - + -
79B VAL* 3.9 42.8 - - + -
87B GLY* 4.6 10.5 - - - -
88B ILE 3.2 6.0 + - - +
89B VAL* 3.3 18.0 - - + +
90B VAL 2.8 26.8 + - - +
114B MET* 4.7 2.9 - - - -
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Residues in contact with TYR 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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25B TRP* 3.5 40.8 - + + -
30B LEU* 3.9 8.1 - - + -
49B ASP* 3.0 20.2 + - + +
50B PHE* 4.8 8.3 - + + -
58B ILE* 4.1 3.1 - - + -
59B LEU* 1.3 72.0 - - - +
61B VAL* 1.3 77.4 + - - +
62B THR* 4.2 10.7 + - - -
65B ASP* 5.6 0.3 - - - +
75B ARG* 3.2 23.0 + - - -
90B VAL* 3.4 22.9 - - + +
92B GLU* 2.7 40.2 + - + +
119B VAL* 4.3 2.9 - - + +
122B GLN* 3.2 20.4 - - + +
125B ALA* 3.7 25.1 - - + +
129B VAL* 6.2 2.0 - - + -
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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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59B LEU 4.5 1.1 - - - +
60B TYR* 1.3 82.1 - - - +
62B THR* 1.3 58.7 + - - +
65B ASP* 3.4 20.0 - - - +
66B LEU* 3.8 22.2 - - + -
72B TYR* 4.0 33.9 - - + -
75B ARG* 5.1 0.9 - - - +
76B LEU* 5.0 4.0 - - + -
89B VAL* 3.9 23.3 - - + -
90B VAL 2.8 12.4 + - - +
91B VAL* 3.4 11.1 - - + -
92B GLU* 2.9 30.5 + - - +
104B LEU* 4.6 7.9 - - + -
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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