Contacts of the helix formed by residues 56 - 70 (chain B) in PDB entry 1VI9
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 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A CSD 4.1 11.9 - - - +
53B CSD 5.4 1.6 - - - +
54B VAL 3.5 5.8 - - - +
55B MSE 1.3 89.6 - - + +
57B PRO* 1.3 74.5 - - + +
58B SER* 3.9 15.9 - - - +
59B HIS* 2.9 30.3 + - + +
60B LEU* 3.6 5.7 + - - +
89B GLN* 4.8 0.2 - - - -
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Residues in contact with PRO 57 (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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54B VAL* 5.9 1.6 - - + -
55B MSE 3.5 3.3 - - - +
56B PRO* 1.3 84.0 - - + +
58B SER* 1.3 61.5 + - - +
60B LEU* 3.3 18.8 + - + +
61B THR 3.6 0.3 + - - -
86B SER* 4.1 4.3 - - - +
88B GLU* 3.7 33.4 - - + +
89B GLN* 3.9 23.6 - - + +
92B HIS* 3.0 39.7 + - + +
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Residues in contact with SER 58 (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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56B PRO* 3.9 12.1 - - - +
57B PRO* 1.3 75.9 - - - +
59B HIS* 1.3 59.9 + - - +
61B THR* 3.3 4.8 + - - -
62B GLU* 2.9 42.0 + - - +
92B HIS* 3.6 17.8 - - - -
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Residues in contact with HIS 59 (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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40A GLN* 3.1 54.3 + - - +
52A GLY* 4.0 5.7 - - - -
53A CSD 3.4 29.7 + - + +
55B MSE 3.3 25.7 - - + +
56B PRO* 2.9 26.2 + - + +
58B SER* 1.3 81.2 + - - +
60B LEU* 1.3 68.5 + - + +
62B GLU* 3.1 12.8 + - - +
63B ILE* 2.9 42.3 + - + +
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Residues in contact with LEU 60 (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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8B ILE* 4.4 6.3 - - + -
36B LEU* 3.7 32.3 - - + +
37B ASN 4.1 13.7 - - - +
38B THR* 4.5 5.4 - - + -
55B MSE 4.6 6.3 - - + -
56B PRO 4.0 6.1 - - - +
57B PRO 3.5 11.2 - - - +
58B SER 3.2 0.4 - - - -
59B HIS* 1.3 86.7 - - + +
61B THR* 1.3 61.9 + - - +
63B ILE* 3.4 3.8 + - - +
64B VAL* 3.3 17.5 + - - +
89B GLN* 3.9 38.6 - - + +
92B HIS* 4.9 1.8 - - + -
93B ILE* 4.2 22.0 - - + -
96B ILE* 3.6 22.3 - - + +
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Residues in contact with THR 61 (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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57B PRO 3.6 0.4 + - - -
58B SER* 3.3 9.1 + - - -
59B HIS 3.3 0.2 - - - -
60B LEU* 1.3 77.9 - - - +
62B GLU* 1.3 60.6 + - + +
64B VAL* 3.3 3.8 + - - +
65B GLN* 3.2 42.9 + - + +
92B HIS* 2.5 44.7 + - + +
96B ILE* 4.3 9.1 - - + +
99B GLN* 5.7 0.7 - - - +
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Residues in contact with GLU 62 (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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51A THR* 2.6 34.1 + - + -
52A GLY* 4.5 16.9 + - - +
58B SER* 2.9 31.9 + - - +
59B HIS* 3.1 15.6 + - - +
61B THR* 1.3 73.7 - - + +
63B ILE* 1.3 61.2 + - - +
65B GLN* 3.3 10.0 + - + +
66B GLY 3.1 11.3 + - - -
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Residues in contact with ILE 63 (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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13A VAL* 3.7 31.6 - - + -
40A GLN 3.7 5.2 - - - +
41A PHE 3.5 7.9 - - - +
42A SER* 3.4 32.0 - - - +
51A THR* 3.4 2.7 - - - +
52A GLY* 3.8 8.5 - - - -
36B LEU* 3.8 22.7 - - + -
59B HIS* 2.9 47.4 + - + +
60B LEU 3.5 8.1 - - - +
62B GLU* 1.3 75.9 - - - +
64B VAL* 1.3 64.0 + - - +
66B GLY 3.0 10.4 + - - -
67B ILE* 3.1 17.0 + - + +
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Residues in contact with VAL 64 (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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6B LEU* 4.1 15.3 - - + -
36B LEU* 4.2 7.4 - - + -
60B LEU 3.3 9.0 + - - +
61B THR 3.3 7.4 + - - +
62B GLU 3.3 0.6 - - - -
63B ILE* 1.3 76.5 - - + +
65B GLN* 1.3 58.2 + - - +
67B ILE* 3.2 9.4 + - + +
68B ALA* 2.8 26.9 + - - +
73B LEU* 3.9 28.9 - - + +
96B ILE* 3.6 45.1 - - + -
99B GLN* 4.0 17.0 - - + +
100B VAL* 4.8 0.7 - - + -
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Residues in contact with GLN 65 (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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51A THR* 4.8 4.5 - - + -
61B THR* 3.2 36.5 + - + +
62B GLU* 3.4 14.1 - - - +
63B ILE 3.2 0.2 - - - -
64B VAL* 1.3 77.2 - - - +
66B GLY* 1.4 58.2 + - - +
68B ALA* 3.2 5.8 + - - +
69B ALA* 2.7 30.1 + - - +
99B GLN* 2.8 42.4 + - - +
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Residues in contact with GLY 66 (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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42A SER* 3.7 13.5 - - - -
43A ASN* 3.6 9.6 - - - +
49A LYS* 5.8 0.2 - - - +
50A TRP* 5.2 1.6 - - - -
51A THR* 3.6 21.9 - - - +
62B GLU 3.1 7.5 + - - -
63B ILE 3.0 8.8 + - - -
65B GLN* 1.4 78.8 - - - +
67B ILE* 1.3 59.7 + - - +
69B ALA* 3.2 16.9 + - - +
70B ILE* 3.2 9.9 + - - +
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Residues in contact with ILE 67 (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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13A VAL* 4.1 22.4 - - + -
14A TYR* 3.9 20.6 - - + -
42A SER 3.7 17.7 - - - +
6B LEU* 4.7 5.4 - - + -
34B TRP* 4.1 19.7 - - + -
63B ILE* 3.1 19.0 + - + +
64B VAL* 3.2 10.0 + - + +
66B GLY* 1.3 76.5 - - - +
68B ALA* 1.3 63.4 + - - +
70B ILE* 3.4 11.8 + - - +
72B LYS* 3.2 31.3 + - + -
73B LEU* 3.7 30.9 + - + +
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Residues in contact with ALA 68 (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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64B VAL 2.8 16.7 + - - +
65B GLN* 3.6 7.2 - - - +
67B ILE* 1.3 77.0 - - - +
69B ALA* 1.3 57.7 + - - +
71B ASP* 2.9 23.7 + - - +
73B LEU* 4.0 20.3 - - + +
99B GLN* 3.6 21.1 - - - +
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Residues in contact with ALA 69 (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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49A LYS* 3.4 35.6 + - + -
51A THR* 6.3 0.2 - - + -
65B GLN 2.7 17.0 + - - +
66B GLY* 3.2 11.6 + - - +
68B ALA* 1.3 77.5 - - - +
70B ILE* 1.3 59.9 + - - +
71B ASP* 3.5 1.7 + - - +
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Residues in contact with ILE 70 (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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14A TYR* 3.9 24.7 - - + -
43A ASN* 3.7 34.5 - - + +
47A TYR* 3.5 36.3 - - + -
49A LYS* 3.7 29.2 - - + +
66B GLY 3.2 7.9 + - - +
67B ILE* 3.5 14.6 - - - +
69B ALA* 1.3 75.1 - - - +
71B ASP* 1.3 68.2 + - - +
72B LYS* 3.5 21.5 + - + +
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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