Contacts of the helix formed by residues 71 - 81 (chain B) in PDB entry 5VZU
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 PRO 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1105A LEU* 3.8 22.7 - - + -
1108A ASN* 4.8 4.3 - - - +
69B GLU 3.9 3.4 - - - +
70B LEU* 1.3 90.5 - - + +
72B PRO* 1.3 75.4 - - + +
73B GLU* 3.4 22.4 - - - +
74B LEU* 3.1 33.5 + - + +
75B LEU* 3.1 9.0 + - - +
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Residues in contact with PRO 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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70B LEU 3.6 2.7 - - - +
71B PRO* 1.3 81.3 - - + +
73B GLU* 1.3 68.0 + - + +
75B LEU* 3.0 13.2 + - + +
76B VAL* 2.7 41.6 + - + +
96B LYS* 5.1 8.7 - - - +
100B ILE* 4.7 13.6 - - + +
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Residues in contact with GLU 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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1108A ASN* 5.4 2.1 - - - +
71B PRO* 3.5 20.6 - - - +
72B PRO* 1.3 94.6 - - + +
74B LEU* 1.3 60.1 + - + +
76B VAL* 3.5 9.6 + - - +
77B GLU* 3.0 25.3 + - - +
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Residues in contact with LEU 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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1104A ILE* 4.3 22.7 - - + -
1105A LEU* 4.6 5.4 - - + -
1108A ASN* 3.4 46.0 - - + +
1116A LEU* 4.4 11.0 - - + -
1120A CYS* 5.2 2.0 - - - -
70B LEU* 4.4 7.9 - - + -
71B PRO* 3.1 31.8 + - + +
72B PRO 3.1 0.4 - - - -
73B GLU* 1.3 82.9 - - + +
75B LEU* 1.3 64.1 + - - +
77B GLU* 3.1 25.1 + - - +
78B ILE* 3.0 29.1 + - - +
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Residues in contact with LEU 75 (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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67B LEU* 3.8 40.8 - - + +
70B LEU* 3.7 17.5 - - + +
71B PRO 3.1 8.7 + - - +
72B PRO* 3.0 8.6 + - + +
74B LEU* 1.3 73.3 - - - +
76B VAL* 1.3 60.4 + - - +
78B ILE* 3.2 5.0 + - + -
79B PHE* 2.8 56.4 + - + -
96B LYS* 3.4 29.2 - - - +
97B PHE* 4.5 11.4 - - + -
100B ILE* 3.5 25.4 - - + -
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Residues in contact with VAL 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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72B PRO* 2.7 27.9 + - + +
73B GLU* 3.6 9.2 - - - +
75B LEU* 1.3 73.7 - - - +
77B GLU* 1.3 57.8 - - - +
80B ALA* 2.8 30.8 + - + +
100B ILE* 4.0 19.7 - - + -
103B THR* 4.4 14.4 - - + +
105B THR* 4.2 14.1 - - - +
106B ILE* 3.7 28.1 - - + +
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Residues in contact with GLU 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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1116A LEU* 4.0 20.8 - - - +
1117A ASP* 4.0 16.8 - - - +
1120A CYS* 4.1 15.7 - - + +
73B GLU 3.0 14.8 + - - +
74B LEU* 3.1 26.0 + - - +
76B VAL* 1.3 76.7 - - - +
78B ILE* 1.3 64.2 + - - +
80B ALA* 3.7 6.0 - - - +
81B SER* 3.2 21.4 + - - -
109B ARG* 4.7 6.1 + - - +
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Residues in contact with ILE 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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1104A ILE* 4.6 1.8 - - + -
1120A CYS* 3.8 35.4 - - + +
1123A VAL* 4.2 22.4 - - + -
1124A ALA* 4.2 27.4 - - + +
1127A ILE* 4.6 5.2 - - + -
67B LEU* 4.6 4.9 - - + -
70B LEU* 3.9 26.5 - - + -
74B LEU* 3.0 16.1 + - + +
75B LEU* 3.7 7.6 - - + +
77B GLU* 1.3 76.8 - - - +
79B PHE* 1.3 73.1 + - + +
81B SER* 3.0 24.0 + - - -
82B LEU* 3.7 6.5 + - + +
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Residues in contact with PHE 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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1127A ILE* 4.5 9.0 - - + -
67B LEU* 5.3 3.1 - - + -
75B LEU* 2.8 41.0 + - + +
76B VAL 4.2 2.0 - - - +
78B ILE* 1.3 82.7 - - + +
80B ALA* 1.3 63.3 + - - +
82B LEU* 3.0 26.5 + - + +
87B LEU* 3.6 20.4 - - + +
90B LEU* 3.5 38.8 - - + -
97B PHE* 4.0 38.4 - + + -
100B ILE* 4.0 26.5 - - + -
101B LEU* 4.0 15.7 - - + -
106B ILE* 4.3 12.1 - - + +
110B ARG* 4.8 0.2 - - - -
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Residues in contact with ALA 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 VAL* 2.8 23.7 + - + +
77B GLU* 3.7 6.3 - - - +
78B ILE 3.2 0.2 - - - -
79B PHE* 1.3 77.6 - - - +
81B SER* 1.3 49.7 + - - +
82B LEU 3.3 0.4 - - - -
105B THR 5.7 0.4 - - - -
106B ILE* 4.1 29.3 - - + +
109B ARG* 3.4 26.6 + - + +
110B ARG* 2.7 33.7 + - - +
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Residues in contact with SER 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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1120A CYS 5.2 1.2 + - - -
1121A LYS* 5.4 5.9 - - - +
1124A ALA* 3.7 17.7 - - - +
1128A LYS* 5.4 3.8 - - - -
77B GLU* 3.2 10.3 + - - -
78B ILE* 3.0 18.0 + - - -
79B PHE 3.1 1.4 - - - -
80B ALA* 1.3 77.9 - - - +
82B LEU* 1.3 58.5 + - - +
83B PRO* 4.1 2.1 - - - +
109B ARG* 3.8 18.1 - - - +
110B ARG* 3.9 6.1 + - - +
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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