Contacts of the strand formed by residues 70 - 76 (chain B) in PDB entry 6MZL
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 70 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B SER* 3.5 31.0 - - - +
68B LYS 3.2 21.5 - - - -
69B GLN* 1.3 73.7 - - - +
71B ARG* 1.3 62.6 + - - +
72B ILE* 3.3 16.8 + - + +
86B TYR* 3.4 28.5 + - - +
150B PHE* 5.4 5.6 - - + -
151B SER 4.5 4.9 - - - +
152B LEU* 3.7 23.8 - - + -
187B ARG 4.4 2.0 - - - -
188B PHE 4.8 0.2 - - - -
189B TRP 4.3 8.1 - - - -
191B PRO* 4.5 8.5 - - + -
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Residues in contact with ARG 71 (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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69B GLN 4.1 1.8 + - - -
70B CYS* 1.3 70.5 - - - +
72B ILE* 1.3 72.2 + - - +
73B TYR* 4.1 22.0 - - + -
86B TYR* 5.2 2.5 - - - -
151B SER* 3.1 40.5 + - - +
153B ASP* 4.7 15.8 + - - +
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B SER* 5.1 2.9 - - - +
70B CYS* 3.3 22.6 + - + +
71B ARG* 1.3 87.3 + - - +
73B TYR* 1.3 64.7 + - - +
74B ARG 3.6 14.4 - - - +
75B VAL* 3.8 17.3 - - + -
84B PHE* 3.8 29.5 - - + -
86B TYR* 5.2 1.1 - - + -
126B LEU* 4.9 14.4 - - + -
148B ILE* 3.7 13.5 - - + -
149B ASN 3.3 15.5 - - - +
150B PHE* 3.7 19.1 - - + -
191B PRO* 4.7 12.3 - - + -
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Residues in contact with TYR 73 (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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46B VAL* 4.7 12.0 - - + +
71B ARG* 4.1 26.8 + - - -
72B ILE* 1.3 82.1 - - - +
74B ARG* 1.3 60.7 + - - +
81B GLU* 5.3 0.9 - - - +
149B ASN* 2.7 47.2 + - - +
150B PHE* 3.5 2.7 - - - +
151B SER* 3.1 37.2 + - - -
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Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 3.9 1.6 - - - -
73B TYR* 1.3 77.5 - - - +
75B VAL* 1.3 86.6 + - - +
76B ARG* 3.0 42.5 - - - +
81B GLU* 4.3 22.1 + - - +
147B HIS* 3.5 22.6 + - - -
148B ILE* 3.4 5.2 - - - +
149B ASN* 2.9 47.6 + - + +
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 3.8 12.6 - - + -
74B ARG* 1.3 83.7 - - - +
76B ARG* 1.3 69.4 + - - +
81B GLU* 3.2 28.6 + - + +
82B ALA 4.9 4.7 - - - +
83B ALA 4.7 6.3 - - - +
84B PHE* 3.8 30.1 - - + -
128B ILE* 3.7 35.0 - - + -
146B ILE* 5.1 2.5 - - + -
147B HIS 3.6 2.7 - - - -
148B ILE* 3.8 23.1 - - + -
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Residues in contact with ARG 76 (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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50B GLU* 4.6 4.4 + - - -
74B ARG* 3.0 37.0 - - - +
75B VAL* 1.3 81.4 - - - +
77B ILE* 1.3 71.6 + - - +
78B ASN* 4.0 4.7 - - - +
79B ASP* 2.4 62.6 + - - +
80B LEU 3.5 15.7 - - - +
81B GLU* 4.1 1.6 - - + +
82B ALA 4.9 0.7 - - - +
128B ILE* 5.4 0.2 - - - -
146B ILE* 3.7 2.4 - - - +
147B HIS* 2.8 72.0 + - - +
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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