Contacts of the helix formed by residues 74 - 83 (chain I) in PDB entry 1VQ7
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 74 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11640 U 3.0 25.8 - - - +
72I VAL 3.5 1.1 - - - +
73I PRO* 1.3 88.3 - - + +
75I THR* 1.3 66.1 + - - +
76I ALA* 4.5 7.4 - - + +
77I GLU* 2.9 46.6 + - + +
78I LEU* 3.2 17.7 + - - +
112I LYS* 3.4 1.6 - - - -
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Residues in contact with THR 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11630 G 3.0 25.5 + - - +
11640 U 2.5 16.1 + - - -
74I PRO* 1.3 65.0 - - - +
76I ALA* 1.3 57.2 + - - +
77I GLU 2.7 15.9 + - - -
78I LEU* 3.0 13.6 + - - +
79I ILE* 3.1 34.4 + - + +
108I ILE* 5.2 1.1 - - + -
112I LYS* 2.5 27.7 + - - +
128I VAL* 4.3 19.8 - - + +
131I THR* 4.1 21.3 - - - +
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Residues in contact with ALA 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11640 U 4.6 0.2 + - - -
11660 A 4.4 2.0 - - - +
11670 G 3.0 40.6 - - - +
74I PRO* 3.4 5.1 - - + +
75I THR* 1.3 79.0 - - - +
77I GLU* 1.3 63.8 + - + +
79I ILE* 4.0 9.3 - - - +
80I LYS* 2.8 39.0 + - - +
131I THR* 5.0 7.9 - - + +
135I LEU* 5.4 4.1 - - - +
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Residues in contact with GLU 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I PRO* 4.0 10.9 - - + +
74I PRO* 2.9 43.1 + - - +
75I THR 2.7 4.9 + - - -
76I ALA* 1.3 78.3 - - + +
78I LEU* 1.3 53.9 + - - +
79I ILE 2.6 6.7 + - - -
80I LYS* 2.6 37.9 + - + +
81I ASP* 3.0 18.2 + - - +
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Residues in contact with LEU 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I VAL* 4.7 3.1 - - + -
73I PRO* 4.0 23.1 - - + +
74I PRO 3.2 7.8 + - - +
75I THR* 3.0 7.1 + - - +
77I GLU* 1.3 77.7 - - - +
79I ILE* 1.3 60.4 + - - +
81I ASP* 3.5 20.9 + - - +
82I GLU* 3.7 8.7 + - - +
108I ILE* 3.7 41.0 - - + +
111I GLN* 3.7 31.9 - - + +
112I LYS* 3.3 37.0 - - + +
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Residues in contact with ILE 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I THR* 3.3 36.8 - - + +
76I ALA* 4.0 5.2 - - - +
77I GLU 2.6 4.6 + - - -
78I LEU* 1.3 72.7 - - + +
80I LYS* 1.3 52.7 - - + +
81I ASP 2.8 9.6 + - - -
82I GLU* 3.6 1.5 + - - +
83I ALA* 2.8 40.2 + - + +
100I LEU* 4.3 17.8 - - + +
108I ILE* 4.3 16.2 - - + -
128I VAL* 4.6 1.6 - - + +
131I THR* 4.3 17.0 - - + +
132I CYS* 3.4 26.7 - - - -
135I LEU* 4.7 9.2 - - + -
137I VAL* 4.4 19.5 - - + -
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Residues in contact with LYS 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11670 G 4.0 8.7 + - - -
11680 C 3.2 32.1 + - - -
76I ALA* 2.8 37.1 - - - +
77I GLU* 2.6 22.4 + - + +
79I ILE* 1.3 73.1 - - + +
81I ASP* 1.3 61.7 + - - +
83I ALA* 4.3 3.4 - - - -
84I GLY* 3.5 3.8 + - - -
85I PHE* 2.6 34.2 + - + +
86I GLU* 3.1 24.2 + - - +
87I THR 5.8 0.4 - - - +
88I GLY* 4.9 4.5 - - - +
135I LEU* 5.7 6.3 - - + -
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Residues in contact with ASP 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I GLU* 3.0 24.1 - - - +
78I LEU* 3.5 17.4 + - + +
79I ILE 2.8 2.2 + - - -
80I LYS* 1.3 78.1 - - - +
82I GLU* 1.3 59.8 + - + +
83I ALA 2.8 2.9 - - - -
84I GLY* 2.5 29.3 + - - -
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Residues in contact with GLU 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I LEU 3.7 8.4 + - - +
79I ILE 3.6 1.6 + - - +
81I ASP* 1.3 81.1 - - + +
83I ALA* 1.3 59.1 - - - +
84I GLY* 4.5 0.2 - - - -
99I ASP 5.1 0.3 - - - +
100I LEU* 4.2 7.2 - - + +
104I GLN* 3.5 36.3 - - - +
107I GLN* 3.6 31.9 + - - +
108I ILE* 3.2 32.8 - - + +
111I GLN* 5.8 3.4 - - - -
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Residues in contact with ALA 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I ILE* 2.8 31.3 + - + +
80I LYS* 4.3 2.5 - - - -
81I ASP 2.8 0.6 + - - -
82I GLU* 1.3 79.4 - - - +
84I GLY* 1.3 57.3 - - - +
85I PHE* 2.8 33.3 - - + +
98I ALA* 4.0 22.6 - - + +
99I ASP 4.7 3.4 - - - -
100I LEU* 4.2 11.4 - - + +
137I VAL* 5.5 0.2 - - + -
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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