Contacts of the helix formed by residues 13 - 25 (chain D) in PDB entry 2V5Q
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 ASP 13 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D LEU* 1.3 57.7 + - - +
15D GLY 3.2 2.7 - - - -
16D LYS* 3.0 35.4 + - - +
17D LYS* 2.6 65.6 + - - +
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Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ASP* 1.3 77.1 - - - +
15D GLY* 1.3 62.1 + - - +
17D LYS* 3.9 11.5 - - + +
18D LEU* 3.3 22.7 + - - +
33D LEU* 4.3 18.0 - - + +
36D ASN* 3.7 26.0 - - + +
37D GLY 3.8 4.7 - - - +
38D ALA* 3.5 44.7 - - + +
39D ASP 5.3 0.7 - - - +
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Residues in contact with GLY 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ASP 3.2 0.4 - - - -
14D LEU* 1.3 77.8 - - - +
16D LYS* 1.3 61.5 + - - +
18D LEU* 3.3 7.3 + - - +
19D LEU* 3.0 27.2 + - - +
39D ASP* 4.7 11.1 - - - +
42D ALA* 3.6 24.7 - - - +
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Residues in contact with LYS 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ASP* 3.0 37.7 + - - +
15D GLY* 1.3 72.4 - - - +
17D LYS* 1.3 66.4 + - - +
19D LEU* 3.1 16.4 + - + +
20D GLU* 3.0 47.8 + - + +
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Residues in contact with LYS 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ASP* 2.6 50.7 + - + +
14D LEU* 3.9 10.9 - - + +
16D LYS* 1.3 72.3 - - + +
18D LEU* 1.3 52.1 + - - +
20D GLU* 3.2 12.9 + - - +
21D ALA* 2.8 35.0 + - - +
29D GLU* 5.4 2.2 - - - +
33D LEU* 3.8 31.1 - - + +
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Residues in contact with LEU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU 3.3 14.3 + - - +
15D GLY 3.5 4.9 - - - +
16D LYS 3.2 0.4 - - - -
17D LYS* 1.3 74.4 - - - +
19D LEU* 1.3 57.1 - - - +
21D ALA* 4.3 0.2 - - - -
22D ALA* 2.8 38.1 + - + +
30D VAL* 4.0 38.1 - - + +
33D LEU* 3.8 10.7 - - + +
34D ILE* 4.3 13.9 - - + -
38D ALA* 3.8 17.3 - - + +
39D ASP 3.3 33.2 - - - +
40D VAL* 3.8 11.0 - - + -
50D PRO* 3.8 13.5 - - + -
66D LEU* 4.5 7.2 - - + -
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLY 3.0 22.1 + - - +
16D LYS* 3.4 16.4 - - + +
18D LEU* 1.3 74.9 - - - +
20D GLU* 1.3 59.9 + - + +
22D ALA* 3.8 1.5 - - - +
23D ARG* 3.0 23.6 + - - +
42D ALA* 3.9 10.1 - - + +
43D VAL 3.9 23.3 - - - +
44D ASP* 3.9 12.3 - - + +
48D LEU 3.4 23.8 - - - +
49D THR 3.6 2.7 - - - -
50D PRO* 3.5 29.2 - - + -
53D LEU* 3.4 26.7 - - + +
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Residues in contact with GLU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LYS* 3.0 45.6 + - + +
17D LYS* 3.7 10.8 - - - +
19D LEU* 1.3 76.9 - - + +
21D ALA* 1.3 59.5 + - - +
23D ARG* 3.4 13.4 + - - +
24D ALA* 2.9 31.9 + - - +
26D GLN* 5.3 0.2 - - - -
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Residues in contact with ALA 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LYS 2.8 20.2 + - - +
18D LEU* 3.7 3.6 - - - +
20D GLU* 1.3 74.0 - - - +
22D ALA* 1.3 60.8 + - - +
24D ALA 3.6 0.2 + - - -
25D GLY 3.2 2.8 + - - -
26D GLN* 3.0 39.3 + - - +
29D GLU* 3.8 29.8 - - + -
30D VAL* 3.8 18.1 - - + +
33D LEU* 3.9 7.2 - - + -
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Residues in contact with ALA 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 2.8 18.0 + - + +
19D LEU 3.8 3.4 - - - +
21D ALA* 1.3 76.7 - - - +
23D ARG* 1.3 63.0 + - - +
25D GLY* 3.5 2.1 + - - -
30D VAL* 3.8 10.9 - - + +
50D PRO* 3.6 34.8 - - + +
53D LEU* 4.9 0.2 - - + -
54D ALA* 3.8 11.3 - - + +
59D HIS* 3.3 19.2 - - - -
62D ILE* 4.1 17.4 - - + +
66D LEU* 4.6 0.2 - - + -
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Residues in contact with ARG 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ARG* 4.5 19.1 + - - +
320A THR* 4.6 11.3 + - - +
321A ILE* 5.6 4.8 - - - +
19D LEU 3.0 17.3 + - - +
20D GLU* 3.7 12.6 - - - +
22D ALA* 1.3 72.3 - - - +
24D ALA* 1.3 58.2 + - - +
25D GLY 3.0 4.7 - - - -
44D ASP* 4.3 12.5 + - - -
48D LEU* 4.7 3.8 - - - +
53D LEU* 3.4 47.5 - - + +
56D VAL* 6.0 1.0 - - - +
57D SER* 3.9 12.5 + - - +
59D HIS* 2.9 22.0 + - - -
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Residues in contact with ALA 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D GLU 2.9 18.0 + - - +
21D ALA 4.1 1.3 - - - +
23D ARG* 1.3 77.5 - - - +
25D GLY* 1.3 59.8 + - - +
26D GLN* 3.4 36.7 + - - +
59D HIS* 3.8 5.9 + - - -
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Residues in contact with GLY 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ALA 3.2 2.6 + - - -
23D ARG 3.0 5.3 - - - -
24D ALA* 1.3 79.7 - - - +
26D GLN* 1.3 60.3 + - - +
27D ASP* 3.3 9.5 + - - +
59D HIS* 3.3 34.2 + - - +
62D ILE* 3.5 12.5 - - - +
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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