Contacts of the helix formed by residues 75 - 87 (chain A) in PDB entry 1V9J
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 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A GLY 4.4 2.2 - - - +
74A LYS* 1.3 98.7 - - + +
76A LEU* 1.3 67.2 + - - +
77A LEU* 3.8 19.7 - - + -
78A GLN* 3.2 24.7 + - + +
79A ARG* 3.1 20.3 + - - +
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PRO* 1.3 72.2 - - - +
77A LEU* 1.3 72.8 + - + +
79A ARG* 3.2 50.8 + - - +
80A HIS* 3.7 16.9 + - + +
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PRO* 3.8 19.5 - - + -
76A LEU* 1.3 91.3 - - + +
78A GLN* 1.3 72.9 + - - +
80A HIS* 3.5 5.5 + - - +
81A ARG* 3.1 39.9 + - - +
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Residues in contact with GLN 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LYS* 4.0 20.0 - - + +
75A PRO* 3.2 39.0 + - + +
77A LEU* 1.3 89.5 - - - +
79A ARG* 1.3 58.6 + - - +
81A ARG* 3.8 25.0 + - - +
82A LEU* 2.8 47.7 + - + +
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Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A PHE* 2.9 55.3 + - + +
72A GLU* 3.7 23.0 + - - -
74A LYS* 3.0 18.3 + - + -
75A PRO* 3.1 9.0 + - - +
76A LEU* 3.3 43.0 - - - +
78A GLN* 1.3 76.5 - - - +
80A HIS* 1.3 64.0 + - + +
82A LEU* 3.1 19.8 + - - +
83A VAL* 3.3 13.7 + - - +
101A THR* 3.6 28.2 + - + +
102A LEU* 6.3 0.4 - - - +
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Residues in contact with HIS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LEU* 3.7 16.6 + - + +
77A LEU* 3.5 8.1 + - - +
79A ARG* 1.3 79.2 - - - +
81A ARG* 1.3 62.1 + - - +
83A VAL* 3.3 9.2 + - - +
84A ASN* 2.9 33.2 + - - +
99A GLN* 3.9 32.9 + - + +
100A LYS* 4.5 5.0 - - + +
101A THR* 4.1 30.0 + - + -
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Residues in contact with ARG 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 3.1 33.4 + - - +
78A GLN* 3.9 27.0 + - - +
80A HIS* 1.3 77.3 - - - +
82A LEU* 1.3 56.7 + - - +
84A ASN* 3.3 12.6 + - + +
85A GLU* 2.9 51.6 + - + +
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASP* 5.5 2.2 - - - +
43A LEU* 3.9 27.2 - - + +
70A LYS* 6.0 3.8 - - + -
71A PHE* 4.6 5.6 - - + -
74A LYS* 3.5 36.3 - - + -
78A GLN* 2.8 35.7 + - + +
79A ARG* 3.1 11.6 + - - +
81A ARG* 1.3 76.3 - - - +
83A VAL* 1.3 62.1 + - - +
85A GLU* 3.2 23.5 + - + +
86A CYS* 3.2 13.7 + - - +
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 3.3 39.8 - - + +
43A LEU* 3.8 20.4 - - + -
64A VAL* 4.9 0.2 - - + -
66A VAL* 5.9 2.7 - - + -
71A PHE* 4.4 9.0 - - + -
79A ARG 3.5 15.0 - - - +
80A HIS* 3.3 8.4 + - - +
82A LEU* 1.3 75.5 - - - +
84A ASN* 1.3 60.7 + - - +
86A CYS* 3.6 3.6 + - - +
87A LEU* 3.5 20.7 + - + +
97A PHE* 4.7 2.7 - - + -
99A GLN* 3.4 32.3 + - + +
101A THR* 4.6 8.3 - - + -
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Residues in contact with ASN 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A HIS* 2.9 27.5 + - - +
81A ARG* 3.6 13.1 - - + +
82A LEU 3.2 0.4 - - - -
83A VAL* 1.3 76.3 - - - +
85A GLU* 1.3 65.1 - - + +
87A LEU 3.4 1.7 - - - -
88A ALA* 3.0 25.5 + - - +
91A LEU* 3.6 28.7 - - + +
99A GLN* 3.6 23.5 + - - +
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Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ARG* 2.9 41.0 + - + +
82A LEU* 3.2 16.9 + - + +
84A ASN* 1.3 77.9 - - + +
86A CYS* 1.3 64.0 + - - +
88A ALA* 3.4 17.1 - - - +
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Residues in contact with CYS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LYS* 3.8 34.9 - - - -
39A LEU* 3.7 16.6 - - + -
42A ASP* 3.2 45.8 - - - +
82A LEU 3.2 8.0 + - - +
83A VAL 3.7 8.7 - - - +
84A ASN 3.3 0.2 - - - -
85A GLU* 1.3 81.7 - - - +
87A LEU* 1.3 60.5 + - + +
88A ALA 3.3 3.1 + - - -
89A GLU* 5.0 0.7 + - - +
90A GLU* 4.2 3.6 - - - +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TYR* 5.7 0.2 - - + -
35A LEU* 3.1 43.3 - - + -
38A LYS* 3.4 32.3 - - + -
39A LEU* 4.1 15.0 - - + -
83A VAL 3.5 13.7 + - - +
84A ASN 3.4 4.0 - - - -
86A CYS* 1.3 76.8 - - + +
88A ALA* 1.3 55.4 + - - +
89A GLU 3.3 2.5 - - - -
90A GLU* 3.7 20.4 - - + +
91A LEU* 2.6 42.4 + - + +
94A ILE* 6.3 0.7 - - + -
97A PHE* 3.8 30.1 - - + -
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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