Contacts of the helix formed by residues 19 - 28 (chain A) in PDB entry 2VZ9
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 LEU 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A MET* 3.9 17.0 - - + +
10A SER* 3.8 13.4 + - - -
11A GLY 3.7 19.2 + - - +
13A LEU* 3.5 32.3 - - + -
18A ASN* 1.3 70.3 - - - +
20A GLU* 1.3 59.2 + - - +
22A PHE* 3.7 21.4 + - + +
23A TRP* 3.3 18.5 + - - +
342A ILE* 3.3 36.3 - - + -
346A LEU* 4.0 17.9 - - + +
829A LEU* 4.8 6.6 - - + +
831A SER* 4.5 12.5 + - - +
832A PRO* 4.6 6.5 - - + +
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Residues in contact with GLU 20 (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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18A ASN* 2.8 12.8 + - - +
19A LEU* 1.3 72.1 - - - +
21A GLU* 1.3 66.3 + - - +
22A PHE 3.2 0.2 - - - -
23A TRP* 3.1 18.0 + - + +
24A ALA* 3.2 12.3 + - - +
443A ARG* 5.9 0.9 + - - -
829A LEU* 4.9 12.5 - - + +
832A PRO* 3.7 19.0 - - + +
833A HIS* 3.3 33.1 + - - -
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Residues in contact with GLU 21 (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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15A GLU 4.7 3.8 - - - +
16A SER* 3.4 14.9 - - - -
17A GLU* 2.5 42.2 + - - +
18A ASN* 2.8 25.2 + - - +
20A GLU* 1.3 77.2 - - - +
22A PHE* 1.3 60.1 + - - +
23A TRP 3.1 1.2 + - - -
24A ALA* 3.2 16.7 + - - +
25A ASN* 3.3 18.3 + - - +
55A LYS* 3.7 20.9 + - - +
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Residues in contact with PHE 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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13A LEU* 3.5 44.4 - - + -
16A SER* 3.4 19.2 - - - -
18A ASN 3.2 2.6 + - - -
19A LEU* 3.7 27.8 - - + +
20A GLU 3.2 0.6 - - - -
21A GLU* 1.3 77.5 - - - +
23A TRP* 1.3 58.7 + - - +
25A ASN* 4.2 2.0 - - - -
26A LEU* 3.0 45.8 + - + +
32A MET* 3.5 26.8 - - + +
325A THR* 3.9 23.8 - - + -
329A MET* 4.2 7.6 - - - -
339A ALA 4.7 1.8 - - - -
342A ILE* 4.2 9.6 - - + -
343A LYS* 4.4 7.6 - - - -
346A LEU* 3.6 19.5 - - + -
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Residues in contact with TRP 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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19A LEU 3.3 12.1 + - - +
20A GLU* 3.1 16.0 + - + +
21A GLU 3.0 1.0 - - - -
22A PHE* 1.3 76.7 - - - +
24A ALA* 1.3 73.8 + - - +
25A ASN 3.1 1.1 - - - -
26A LEU* 2.9 29.1 + - + +
27A ILE* 3.0 47.3 + - + +
343A LYS 4.8 0.7 - - - -
346A LEU* 3.6 21.5 - - + -
347A SER* 3.4 42.0 - - - -
350A HIS* 2.7 46.0 + + + +
352A VAL* 3.7 12.3 - - + -
354A ALA* 5.0 4.0 - - + -
829A LEU* 5.9 2.2 - - + -
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Residues in contact with ALA 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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20A GLU 3.2 8.9 + - - +
21A GLU* 3.5 12.3 - - - +
23A TRP* 1.3 82.0 - - - +
25A ASN* 1.3 59.3 + - - +
27A ILE* 3.9 2.3 - - - +
28A GLY* 2.7 34.7 + - - -
30A VAL* 5.6 0.7 - - - -
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Residues in contact with ASN 25 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A PRO 4.0 0.5 - - - +
15A GLU* 3.4 16.2 + - - +
16A SER* 2.9 24.6 + - - -
21A GLU 3.3 11.7 + - - +
22A PHE 4.1 0.9 - - - +
23A TRP 3.1 0.4 - - - -
24A ALA* 1.3 84.3 - - - +
26A LEU* 1.3 65.1 + - - +
29A GLY* 2.9 18.5 + - - -
30A VAL* 3.0 39.7 + - - +
32A MET* 3.1 32.1 - - + +
328A ASN* 4.7 0.5 - - - +
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Residues in contact with LEU 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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22A PHE* 3.0 41.9 + - + +
23A TRP* 2.9 30.2 + - + +
25A ASN* 1.3 80.6 - - - +
27A ILE* 1.3 62.7 + - - +
29A GLY* 3.2 10.0 + - - -
32A MET* 3.9 12.1 - - + -
325A THR* 4.2 9.4 - - + -
328A ASN* 3.7 37.5 - - + +
343A LYS* 4.1 15.7 - - + -
346A LEU* 3.9 4.9 - - + -
354A ALA* 4.0 17.9 - - + -
355A PRO* 3.8 14.6 - - - +
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Residues in contact with ILE 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 TRP* 3.0 57.7 + - + +
24A ALA* 4.0 2.0 - - - +
26A LEU* 1.3 75.2 - - - +
28A GLY* 1.3 62.3 + - - +
29A GLY* 2.9 10.4 + - - -
352A VAL* 4.3 16.2 - - + -
353A TRP 4.0 19.3 - - - +
354A ALA* 4.9 0.4 - - - -
355A PRO* 4.3 18.2 - - + +
380A PRO* 5.0 9.9 - - + +
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Residues in contact with GLY 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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24A ALA 2.7 20.6 + - - -
25A ASN 3.7 0.2 - - - -
27A ILE* 1.3 75.5 - - - +
29A GLY* 1.3 69.1 + - - +
30A VAL* 3.6 9.9 - - - +
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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