Contacts of the helix formed by residues 56 - 70 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C VAL* 3.5 8.0 - - + +
55C MSE 1.3 93.7 - - + +
57C PRO* 1.3 70.3 - - + +
58C SER* 4.0 14.4 - - - +
59C HIS* 2.9 34.0 + - + +
60C LEU* 3.7 2.9 + - - +
53D CSD 5.5 1.8 - - - +
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Residues in contact with PRO 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C VAL* 6.2 0.9 - - + -
55C MSE 3.4 3.3 - - - +
56C PRO* 1.3 85.8 - - + +
58C SER* 1.3 60.2 + - - +
60C LEU* 3.1 31.5 + - + +
61C THR 3.4 0.9 + - - -
86C SER* 4.6 2.2 - - - +
88C GLU* 3.9 31.0 - - + +
89C GLN* 4.0 26.9 - - + +
92C HIS* 3.2 38.8 + - + +
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Residues in contact with SER 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C PRO* 4.0 12.5 - - - +
57C PRO* 1.3 76.0 - - - +
59C HIS* 1.3 61.9 + - - +
61C THR* 3.4 4.0 + - - -
62C GLU* 2.9 30.8 + - - +
92C HIS* 3.7 17.8 + - - -
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Residues in contact with HIS 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LEU* 4.5 2.2 - - + -
55C MSE 3.1 28.8 - - + +
56C PRO* 2.9 27.0 + - + +
58C SER* 1.3 81.3 + - - +
60C LEU* 1.3 67.6 + - + +
62C GLU* 3.1 12.3 + - - +
63C ILE* 2.9 49.7 + - + +
40D GLN* 2.8 41.2 + - - -
52D GLY* 3.8 9.3 - - - -
53D CSD 2.9 25.0 + - - +
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ILE* 4.2 13.2 - - + -
36C LEU* 3.6 39.9 - - + +
37C ASN 4.2 2.9 - - - +
38C THR* 4.1 31.6 - - + -
55C MSE 4.8 3.8 - - + +
56C PRO 4.2 5.8 - - - +
57C PRO* 3.1 20.6 + - + +
59C HIS* 1.3 83.8 - - + +
61C THR* 1.3 62.3 + - - +
63C ILE* 3.2 10.6 + - - +
64C VAL* 3.2 12.3 + - - +
89C GLN* 4.4 17.9 - - + +
92C HIS* 4.8 3.4 - - + -
93C ILE* 4.5 11.7 - - + -
96C ILE* 4.0 14.4 - - + -
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Residues in contact with THR 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C PRO 3.4 0.2 + - - -
58C SER* 3.5 9.6 - - - +
60C LEU* 1.3 78.3 - - - +
62C GLU* 1.3 61.8 + - + +
64C VAL* 3.4 2.8 + - - +
65C GLN* 2.4 56.1 + - - +
92C HIS* 2.6 42.6 + - + +
96C ILE* 4.2 11.3 - - + +
99C GLN* 5.6 1.8 - - - +
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Residues in contact with GLU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C SER 2.9 15.6 + - - +
59C HIS* 3.1 15.2 + - - +
61C THR* 1.3 75.8 - - + +
63C ILE* 1.3 68.3 + - - +
65C GLN* 3.0 14.4 + - + +
66C GLY 2.9 12.6 + - - -
51D THR* 2.9 26.5 + - + -
52D GLY* 3.1 32.6 + - - +
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Residues in contact with ILE 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LEU* 3.9 18.6 - - + -
59C HIS* 2.9 37.7 + - + +
60C LEU 3.2 8.5 + - - +
62C GLU* 1.3 75.6 - - - +
64C VAL* 1.3 60.6 + - + +
66C GLY 2.9 2.6 + - - -
67C ILE* 2.9 30.7 + - + +
13D VAL* 3.8 31.4 - - + -
40D GLN* 3.8 4.3 - - + +
41D PHE 3.7 6.1 - - - +
42D SER* 3.3 31.8 - - - +
51D THR* 3.4 3.1 - - - +
52D GLY* 3.6 25.6 - - - -
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Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 3.9 16.8 - - + -
36C LEU* 4.1 6.1 - - + -
60C LEU 3.2 11.5 + - - +
61C THR 3.7 7.6 - - - +
62C GLU 3.2 0.2 - - - -
63C ILE* 1.3 78.5 - - + +
65C GLN* 1.3 59.0 + - - +
67C ILE* 3.1 12.0 + - + +
68C ALA* 2.8 26.9 + - - +
73C LEU* 3.9 18.6 - - + +
96C ILE* 3.8 36.6 - - + -
99C GLN* 3.7 30.7 - - + +
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Residues in contact with GLN 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C THR* 2.4 53.0 + - - +
62C GLU* 3.0 16.1 + - + +
64C VAL* 1.3 77.7 - - - +
66C GLY* 1.3 63.4 + - - +
68C ALA* 3.3 2.7 + - - +
69C ALA* 3.0 25.1 + - - +
99C GLN* 3.4 31.1 + - - +
51D THR* 4.8 4.3 - - + -
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Residues in contact with GLY 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C GLU 2.9 10.5 + - - -
63C ILE 2.9 5.1 + - - -
65C GLN* 1.3 77.4 - - - +
67C ILE* 1.3 60.7 + - - +
69C ALA* 3.2 18.2 + - - +
70C ILE* 3.2 15.6 + - - +
42D SER* 3.6 13.5 - - - -
43D ASN* 3.7 3.3 - - - +
50D TRP* 5.3 1.6 - - - -
51D THR* 3.5 24.2 - - - +
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Residues in contact with ILE 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 4.8 5.6 - - + -
34C TRP* 4.1 26.2 - - + -
63C ILE* 2.9 30.9 + - + +
64C VAL* 3.5 13.9 - - + +
66C GLY* 1.3 76.1 - - - +
68C ALA* 1.3 61.7 + - - +
70C ILE* 3.4 14.1 - - - +
72C LYS* 3.3 25.7 + - + -
73C LEU* 3.8 28.0 - - + +
13D VAL* 4.3 11.0 - - + -
14D TYR* 4.0 19.1 - - + -
42D SER* 3.8 17.7 - - - +
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Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C VAL 2.8 19.8 + - - +
65C GLN* 3.9 4.7 - - + +
67C ILE* 1.3 72.5 - - - +
69C ALA* 1.3 53.8 + - - +
71C ASP* 2.8 25.9 + - - +
73C LEU* 4.1 22.4 - - + +
99C GLN* 3.8 17.7 - - - +
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Residues in contact with ALA 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C GLN 3.0 17.9 + - - +
66C GLY* 3.2 10.7 + - - +
68C ALA* 1.3 75.9 - - - +
70C ILE* 1.3 60.8 + - - +
71C ASP* 3.5 1.7 + - - +
49D LYS* 3.3 35.0 + - + +
51D THR* 6.2 0.7 - - + -
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Residues in contact with ILE 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C GLY 3.2 9.1 + - - +
67C ILE* 3.4 16.6 - - - +
68C ALA 3.2 0.2 - - - -
69C ALA* 1.3 77.2 - - - +
71C ASP* 1.3 69.6 + - - +
72C LYS* 3.4 33.3 + - + +
14D TYR* 3.9 12.3 - - + -
43D ASN* 3.6 37.2 - - + +
47D TYR* 3.7 46.5 - - + -
49D LYS* 4.2 20.2 - - + +
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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