Contacts of the helix formed by residues 70 - 81 (chain B) in PDB entry 3Q41
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 ASN 70 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ASP* 6.1 1.4 - - - +
68B LYS* 3.3 2.5 - - + +
69B PRO* 1.3 77.5 - - + +
71B ALA* 1.3 53.6 + - - +
72B ILE* 2.8 13.2 + - - +
73B GLN* 2.7 62.4 + - + +
74B MET 3.0 9.1 + - - -
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Residues in contact with ALA 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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109A TYR* 4.9 1.2 + - - -
69B PRO 3.2 9.5 + - - +
70B ASN* 1.3 70.1 - - - +
72B ILE* 1.3 59.9 + - - +
74B MET* 3.9 10.8 - - - -
75B ALA* 3.2 23.7 + - - +
102B PHE 5.8 0.4 - - - +
103B THR* 6.1 3.1 - - + -
105B THR* 5.7 0.7 - - - +
106B PRO* 3.4 25.5 - - + +
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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
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102A PHE* 3.6 39.3 - - + -
105A THR* 5.8 6.1 - - + -
109A TYR* 5.9 0.2 - - - -
127A ILE* 3.5 44.0 - - + -
133A ILE* 5.7 0.2 - - - +
171A HIS* 4.3 14.6 - - + -
70B ASN* 2.8 16.0 + - - +
71B ALA* 1.3 72.6 - - - +
73B GLN* 1.3 63.0 - - - +
75B ALA* 3.2 5.4 + - - +
76B LEU* 2.9 36.9 + - + +
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Residues in contact with GLN 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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170A ASP* 5.0 1.0 - - - +
171A HIS* 3.7 25.3 - - - +
174A ARG* 3.2 29.4 + - - +
68B LYS* 4.2 19.9 + - + +
70B ASN* 2.7 33.8 + - + +
72B ILE* 1.3 77.5 - - - +
74B MET* 1.3 56.2 + - - +
76B LEU* 3.6 18.5 + - - +
77B SER* 3.1 27.0 + - - -
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Residues in contact with MET 74 (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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32B VAL* 3.6 31.4 - - + -
65B VAL* 6.0 0.4 - - - -
67B HIS* 3.9 6.7 - - + -
68B LYS* 3.2 57.3 - - - +
70B ASN 3.0 9.1 + - - +
71B ALA* 4.0 7.0 - - - +
73B GLN* 1.3 74.3 - - - +
75B ALA* 1.3 66.9 + - - +
77B SER* 3.0 16.2 + - - -
78B VAL* 3.1 16.2 + - - +
92B VAL* 5.3 2.2 - - + -
93B SER 5.6 0.4 - - - +
103B THR* 3.8 19.5 - - - +
106B PRO* 3.7 20.4 - - + -
107B VAL* 3.8 16.2 - - + -
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A TYR* 3.3 26.7 - - - +
133A ILE* 3.6 19.8 - - + +
71B ALA 3.2 14.4 + - - +
72B ILE* 3.2 6.3 + - - +
74B MET* 1.3 80.1 - - - +
76B LEU* 1.3 61.1 + - - +
77B SER 3.5 0.2 + - - -
78B VAL* 3.6 9.4 + - - +
79B CYS* 3.7 7.8 + - - +
106B PRO* 3.7 11.2 - - + -
110B THR* 3.4 21.6 + - - +
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Residues in contact with LEU 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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127A ILE* 4.0 9.6 - - + -
130A ASP* 3.4 32.5 - - - +
133A ILE* 4.6 10.1 - - + -
171A HIS* 3.8 28.0 - - + +
72B ILE* 2.9 30.8 + - + +
73B GLN* 3.7 21.5 - - - +
74B MET 3.1 0.2 - - - -
75B ALA* 1.3 78.4 - - - +
77B SER* 1.3 56.0 + - - +
79B CYS* 3.5 5.9 + - + +
80B GLU* 3.1 46.8 + - + +
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Residues in contact with SER 77 (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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65B VAL* 3.6 18.6 - - - +
68B LYS* 3.5 25.9 + - - -
73B GLN 3.1 13.6 + - - -
74B MET* 3.0 11.7 + - - -
76B LEU* 1.3 75.8 - - - +
78B VAL* 1.3 59.1 + - - +
79B CYS 3.2 0.2 - - - -
80B GLU* 4.4 4.5 - - - +
81B ASP* 2.7 55.2 + - - +
82B LEU* 5.2 0.4 - - - -
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Residues in contact with VAL 78 (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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32B VAL* 5.2 2.0 - - + -
74B MET* 3.1 16.8 + - - +
75B ALA* 3.8 8.1 - - - +
76B LEU 3.4 0.2 - - - -
77B SER* 1.3 74.9 - - - +
79B CYS* 1.3 58.1 + - - +
82B LEU* 3.3 19.0 + - + +
83B ILE* 2.8 43.8 + - + +
90B ILE* 3.7 24.0 - - + -
107B VAL* 3.8 38.8 - - + -
110B THR* 4.0 13.9 - - + -
111B ALA 4.6 2.5 - - - +
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Residues in contact with CYS 79 (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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132A SER* 3.6 24.7 - - - -
133A ILE* 4.5 2.5 - - + -
75B ALA 3.7 5.2 + - - +
76B LEU* 3.5 9.7 + - + +
77B SER 3.2 0.6 - - - -
78B VAL* 1.3 77.3 - - - +
80B GLU* 1.3 66.8 + - + +
81B ASP 3.4 0.2 + - - -
84B SER* 3.2 27.7 + - - -
110B THR* 3.7 19.5 - - - -
308B CYS* 2.0 55.3 - - + +
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Residues in contact with GLU 80 (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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76B LEU* 3.1 34.4 + - + +
77B SER* 4.3 4.3 - - - +
79B CYS* 1.3 81.3 - - + +
81B ASP* 1.3 67.9 + - - +
84B SER* 3.0 14.5 + - - -
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Residues in contact with ASP 81 (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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63B THR* 4.4 6.1 + - - -
64B SER 5.8 0.7 - - - +
65B VAL* 3.7 18.2 - - + +
68B LYS* 4.7 2.3 + - - -
77B SER* 2.7 39.4 + - - +
80B GLU* 1.3 86.1 - - - +
82B LEU* 1.3 73.5 + - + +
84B SER* 3.8 5.2 + - - -
85B SER* 3.8 11.4 + - - -
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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