Contacts of the helix formed by residues 13 - 23 (chain C) in PDB entry 1VBF
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 THR 13 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE* 3.3 3.3 - - - +
12C LYS* 1.3 74.1 - - - +
14C GLN* 1.3 58.9 + - - +
15C GLU* 3.9 9.4 - - + +
16C LEU* 2.8 45.8 + - + +
17C ALA 3.1 4.9 + - - -
63C LEU 5.6 0.4 - - - -
64C ASP* 2.9 30.1 + - - -
67C ASP* 4.3 10.6 + - - -
68C LEU* 3.4 33.6 + - + +
69C HIS* 4.5 7.1 - - + -
91C ILE* 5.7 0.2 - - + -
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Residues in contact with GLN 14 (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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11C ILE 5.8 0.2 - - - -
12C LYS 3.1 8.7 + - - +
13C THR* 1.3 70.6 - - - +
15C GLU* 1.3 69.3 + - + +
17C ALA* 2.9 20.2 + - + +
18C GLU* 3.0 32.8 + - + +
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Residues in contact with GLU 15 (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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13C THR* 3.3 7.0 - - + +
14C GLN* 1.3 83.2 + - + +
16C LEU* 1.3 57.4 + - - +
18C GLU* 3.8 17.5 + - - +
19C ALA* 3.0 28.9 + - - +
68C LEU 3.9 4.4 - - - +
69C HIS* 3.5 41.8 + - - +
70C LYS* 3.6 10.3 + - + +
91C ILE* 3.6 28.3 - - + +
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Residues in contact with LEU 16 (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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11C ILE* 3.5 26.9 - - + -
13C THR* 2.8 26.9 + - + +
15C GLU* 1.3 77.5 - - - +
17C ALA* 1.3 56.6 + - - +
19C ALA* 3.3 5.5 + - + -
20C PHE* 2.8 32.3 + - + +
60C ILE* 3.7 13.5 - - + +
63C LEU* 4.3 28.7 - - + +
64C ASP* 3.6 30.7 - - + +
68C LEU* 5.1 2.0 - - + -
87C LEU* 4.8 8.7 - - + -
91C ILE* 4.0 17.2 - - + +
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Residues in contact with ALA 17 (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 LEU* 3.8 23.1 - - + +
9C ARG* 4.9 6.5 - - - +
11C ILE* 3.5 28.4 - - + +
13C THR 3.1 5.3 + - - +
14C GLN* 2.9 14.2 + - + +
16C LEU* 1.3 77.1 - - - +
18C GLU* 1.3 63.0 + - + +
20C PHE* 3.2 4.0 + - - +
21C ASN* 2.9 27.1 + - - +
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Residues in contact with GLU 18 (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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14C GLN* 3.0 31.0 + - + +
15C GLU* 3.8 19.8 - - - +
17C ALA* 1.3 76.8 - - + +
19C ALA* 1.3 57.6 + - - +
21C ASN* 2.9 10.0 + - - +
22C LYS* 2.8 29.3 + - - +
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Residues in contact with ALA 19 (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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15C GLU 3.0 19.0 + - - +
16C LEU* 3.6 4.5 - - + +
18C GLU* 1.3 74.5 - - - +
20C PHE* 1.3 63.9 + - - +
22C LYS* 2.9 17.4 + - - +
23C VAL* 2.9 15.1 + - - +
87C LEU* 3.4 35.9 - - + +
90C GLU* 3.9 18.6 - - + -
91C ILE* 4.2 5.4 - - + -
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Residues in contact with PHE 20 (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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4C LYS* 3.6 41.8 + - + -
7C ILE* 4.3 11.2 - - + -
8C LEU* 4.0 25.8 - - + -
11C ILE* 4.0 17.3 - - + -
16C LEU* 2.8 22.1 + - + +
17C ALA 3.4 3.8 - - - +
19C ALA* 1.3 73.7 - - - +
21C ASN* 1.3 62.0 + - - +
23C VAL 4.1 10.4 - - - +
38C TYR* 3.9 25.6 + + - -
56C LEU* 3.7 25.1 - - + -
60C ILE* 3.6 15.0 - - + -
83C TYR* 3.3 25.4 - - - -
87C LEU* 3.7 9.8 - - + +
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Residues in contact with ASN 21 (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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4C LYS* 3.6 22.2 + - - +
8C LEU* 3.0 41.4 - - - +
9C ARG* 6.1 0.2 - - - -
17C ALA 2.9 10.8 + - - +
18C GLU* 3.3 11.4 - - - +
20C PHE* 1.3 80.4 - - - +
22C LYS* 1.3 59.2 + - - +
23C VAL 5.1 0.5 - - - +
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Residues in contact with LYS 22 (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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113B SER 4.9 10.3 + - - -
114B TYR* 5.9 1.6 + - - +
115B TYR 5.9 0.6 + - - -
116B ASN* 5.4 13.6 - - - +
18C GLU 2.8 14.1 + - - +
19C ALA* 2.9 6.3 + - - +
21C ASN* 1.3 79.4 - - - +
23C VAL* 1.3 63.5 + - + +
24C ASP* 3.4 4.7 + - - +
90C GLU* 2.7 40.8 + - - +
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Residues in contact with VAL 23 (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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19C ALA 2.9 9.9 + - - +
20C PHE 4.1 6.8 - - - +
21C ASN 5.1 0.4 - - - +
22C LYS* 1.3 71.0 - - + +
24C ASP* 1.3 64.2 + - - +
25C ARG 3.2 4.3 + - - -
28C PHE* 3.5 34.3 - - + -
38C TYR* 3.2 10.0 + - - -
83C TYR* 3.9 15.8 - - + -
86C ALA* 4.1 9.0 - - + +
87C LEU* 3.6 26.7 - - + -
90C GLU* 3.7 28.5 - - + +
115C TYR* 3.9 11.4 - - - +
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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