Contacts of the helix formed by residues 21 - 33 (chain A) in PDB entry 2V1C
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 GLY 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A SER* 4.7 0.2 - - - -
20A ILE* 1.3 74.0 - - - +
22A PRO* 1.3 63.5 - - - -
23A LYS* 3.2 5.2 - - - -
24A SER* 2.6 33.6 + - - -
25A ALA* 2.8 16.1 + - - -
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Residues in contact with PRO 22 (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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11A ILE* 4.2 8.0 - - + +
15A SER* 4.4 13.6 - - - +
20A ILE 4.7 0.2 - - - +
21A GLY* 1.3 81.8 - - - -
23A LYS* 1.3 74.4 + - + +
25A ALA* 3.5 8.6 - - + +
26A GLN* 3.0 24.9 + - - +
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Residues in contact with LYS 23 (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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21A GLY* 4.8 2.5 - - - -
22A PRO* 1.3 83.9 - - + +
24A SER* 1.3 56.4 + - - +
26A GLN* 3.5 6.7 + - - +
27A ARG* 2.8 38.1 + - + +
66C ASN* 5.0 12.9 - - - +
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Residues in contact with SER 24 (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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19A GLY 5.2 0.2 + - - -
20A ILE* 4.2 16.8 - - - +
21A GLY* 2.6 28.9 + - - -
23A LYS* 1.3 73.5 - - - +
25A ALA* 1.3 57.6 + - - -
27A ARG* 3.4 10.7 + - - +
28A LEU* 2.9 31.7 + - - +
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Residues in contact with ALA 25 (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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11A ILE* 3.4 33.0 - - + +
14A LEU* 3.8 8.3 - - + +
15A SER* 3.8 19.1 - - - +
20A ILE* 4.1 8.0 - - + +
21A GLY 2.8 14.1 + - - +
22A PRO 3.1 7.8 + - - +
24A SER* 1.3 69.8 - - - +
26A GLN* 1.3 55.1 + - - +
28A LEU* 2.9 8.1 + - - +
29A ALA* 2.7 34.3 + - - +
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Residues in contact with GLN 26 (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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7A LEU* 5.7 0.9 - - + -
11A ILE* 3.4 23.5 - - + +
22A PRO 3.0 15.1 + - - +
23A LYS* 3.8 5.8 - - - +
25A ALA* 1.3 74.4 - - - +
27A ARG* 1.3 85.6 + - - +
29A ALA* 2.9 12.3 + - - +
30A PHE* 3.0 45.9 + - + -
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Residues in contact with ARG 27 (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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23A LYS* 2.8 28.7 + - + +
24A SER* 3.6 10.8 - - - +
25A ALA 3.2 0.2 - - - -
26A GLN* 1.3 93.3 - - - +
28A LEU* 1.3 59.3 + - - +
30A PHE* 3.7 7.0 + - - +
31A HIS* 3.6 18.2 + - - +
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Residues in contact with LEU 28 (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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14A LEU* 3.3 38.1 - - + -
20A ILE* 4.6 20.4 - - + -
24A SER* 2.9 18.5 + - - +
25A ALA* 2.9 12.9 + - - +
27A ARG* 1.3 76.5 - - - +
29A ALA* 1.3 63.7 + - - +
31A HIS* 3.2 12.8 + - + +
32A LEU* 3.2 37.5 + - + +
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Residues in contact with ALA 29 (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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7A LEU* 3.5 17.4 - - + +
10A LEU* 4.0 26.8 - - + +
11A ILE* 3.3 32.1 - - + -
14A LEU* 4.1 2.0 - - + +
25A ALA 2.7 9.8 + - - +
26A GLN 2.9 2.4 + - - +
28A LEU* 1.3 72.7 - - - +
30A PHE* 1.3 63.6 + - - +
31A HIS 3.1 0.2 - - - -
32A LEU* 3.3 6.2 + - - +
33A PHE* 3.2 21.3 + - - +
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Residues in contact with PHE 30 (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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2A LYS* 5.3 7.2 - - - -
7A LEU* 3.6 37.5 - - + -
26A GLN* 3.0 51.2 + - + +
27A ARG* 4.2 6.5 - - - +
29A ALA* 1.3 77.4 - - + +
31A HIS* 1.3 58.5 + - - +
33A PHE* 3.8 26.0 - + + +
34A GLU* 3.6 16.3 + - - +
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Residues in contact with HIS 31 (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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27A ARG 3.6 11.9 + - - +
28A LEU* 3.2 18.8 + - + +
29A ALA 3.1 0.6 - - - -
30A PHE* 1.3 75.9 - - - +
32A LEU* 1.3 77.7 + - + +
33A PHE 3.1 2.0 - - - -
34A GLU* 3.3 14.5 + - - +
35A GLN* 3.1 52.2 + - + +
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Residues in contact with LEU 32 (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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10A LEU* 4.0 28.9 - - + -
14A LEU* 4.1 8.1 - - + -
28A LEU* 3.2 34.0 + - + +
29A ALA* 3.6 7.6 - - - +
31A HIS* 1.3 88.1 - - + +
33A PHE* 1.3 62.5 + - - +
35A GLN* 3.3 20.6 + - + +
40A ILE* 3.7 26.1 - - + +
43A LEU* 4.1 26.7 - - + -
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Residues in contact with PHE 33 (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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29A ALA 3.2 14.8 + - - +
30A PHE* 3.8 23.1 - + + +
32A LEU* 1.3 78.5 - - - +
34A GLU* 1.3 67.9 + - + +
35A GLN 3.1 7.8 + - - +
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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