Contacts of the helix formed by residues 15 - 29 (chain D) in PDB entry 2VUU
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 15 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D ASN* 2.7 23.7 + - - -
14D THR* 1.3 75.1 - - - +
16D ARG* 1.3 67.0 + - - -
17D GLN 3.3 0.8 + - - -
18D ALA 3.4 2.0 + - - -
19D ALA* 2.9 21.7 + - - +
1353D NAP 3.1 36.3 + - - -
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Residues in contact with ARG 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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14D THR 3.7 0.4 + - - -
15D GLY* 1.3 70.8 - - - -
17D GLN* 1.3 64.9 + - - +
19D ALA* 4.3 3.0 - - - +
20D SER* 3.2 21.7 + - - -
23D ARG* 5.7 0.2 + - - -
153D TYR* 3.2 22.8 - - + -
155D ASN* 2.6 41.9 + - - +
156D ASN* 3.2 25.5 + - - +
192D ALA* 3.8 21.5 - - + +
193D GLU* 4.2 25.5 - - + +
1353D NAP 2.8 53.8 + - - +
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Residues in contact with GLN 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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16D ARG* 1.3 78.7 - - - +
18D ALA* 1.3 66.7 + - - +
20D SER* 3.2 8.7 + - - -
21D LEU* 3.2 9.7 + - - +
78D PHE* 3.2 26.2 - - + -
80D ASN* 3.2 25.3 + - - +
111D SER* 2.7 24.8 + - - -
148D VAL* 4.9 1.4 - - - +
150D ALA* 4.0 17.8 - - + +
153D TYR* 3.0 29.6 + - + +
192D ALA* 5.4 0.2 - - + -
196D VAL* 3.2 31.6 - - + +
218D LEU* 5.6 1.7 - - - +
1353D NAP 3.1 18.2 + - - +
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Residues in contact with ALA 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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10D VAL* 3.5 26.9 - - + -
11D VAL 3.8 3.1 - - - +
12D ASN* 3.4 25.6 - - + +
13D ALA* 3.7 5.6 - - - -
15D GLY 3.4 1.8 + - - +
17D GLN* 1.3 78.4 - - - +
19D ALA* 1.3 65.4 + - - +
21D LEU* 2.9 5.7 + - - +
22D ILE* 2.8 26.5 + - - +
78D PHE* 3.8 13.6 - - + -
80D ASN* 5.1 3.7 - - + +
1353D NAP 4.5 0.4 + - - -
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Residues in contact with ALA 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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13D ALA 3.2 15.1 + - - +
14D THR 4.2 7.2 - - - +
15D GLY 2.9 22.2 + - - +
16D ARG* 4.3 3.4 - - - +
18D ALA* 1.3 72.9 - - - +
20D SER* 1.3 63.5 + - - +
22D ILE* 3.6 6.0 - - - +
23D ARG* 2.9 51.4 + - - +
43D ILE* 4.3 11.2 - - + -
47D LEU* 4.5 5.6 - - + -
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Residues in contact with SER 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 ARG 3.2 12.0 + - - -
17D GLN 3.2 11.4 + - - -
18D ALA 3.1 0.2 - - - -
19D ALA* 1.3 81.0 - - - +
21D LEU* 1.3 66.5 + - - +
23D ARG* 3.3 14.9 + - - +
24D VAL* 3.2 22.0 + - - +
192D ALA 3.4 14.7 + - - -
193D GLU* 3.1 20.2 + - - -
196D VAL* 3.9 0.4 - - - -
197D GLY* 2.5 29.8 + - - -
198D PRO* 4.2 1.0 - - - +
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Residues in contact with LEU 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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8D ILE* 4.2 15.7 - - + -
10D VAL* 3.8 19.1 - - + -
17D GLN 3.2 6.8 + - - +
18D ALA 2.9 8.2 + - - +
20D SER* 1.3 78.2 + - - +
22D ILE* 1.3 55.8 + - + +
24D VAL* 3.1 4.0 + - + +
25D ALA* 2.6 51.9 + - + +
32D VAL* 6.1 0.4 - - + -
78D PHE* 3.5 37.0 - - + -
197D GLY* 3.5 16.3 - - - +
200D LEU* 4.2 27.4 - - + -
201D LEU* 4.9 7.4 - - + +
204D PHE* 4.6 7.0 - - + -
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Residues in contact with ILE 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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10D VAL* 4.5 15.3 - - + -
13D ALA* 3.6 42.4 - - + +
18D ALA 2.8 20.7 + - - +
19D ALA* 3.6 5.6 - - - +
21D LEU* 1.3 74.8 - - + +
23D ARG* 1.3 59.4 + - - +
25D ALA* 4.3 3.6 - - - -
26D ALA* 2.8 31.5 + - - +
32D VAL* 4.1 16.7 - - + +
34D ALA* 3.9 15.0 - - + -
47D LEU* 4.1 18.6 - - + -
50D ILE* 4.7 1.6 - - + -
53D VAL* 3.9 28.3 - - + -
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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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19D ALA* 2.9 36.3 + - - +
20D SER* 3.7 23.4 - - - +
22D ILE* 1.3 74.5 - - - +
24D VAL* 1.3 64.9 + - + +
26D ALA* 3.6 2.0 + - - +
27D ALA* 3.0 25.8 + - - +
43D ILE* 3.7 26.1 - - - +
46D GLU* 3.0 25.2 + - - +
47D LEU* 4.8 4.4 - - + +
50D ILE* 4.5 20.3 - - + +
193D GLU* 4.1 24.0 + - - +
709L PRO* 3.7 20.2 + - + +
710L LEU 4.2 16.4 - - - -
711L SER* 3.3 30.8 + - - +
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Residues in contact with VAL 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 SER* 3.2 13.0 + - - +
21D LEU 3.1 6.8 + - - +
23D ARG* 1.3 77.9 - - + +
25D ALA* 1.3 62.6 + - - +
27D ALA* 3.3 3.5 + - - +
28D VAL* 3.2 24.4 + - - +
193D GLU 6.0 0.7 - - - +
197D GLY 4.2 13.2 - - - +
198D PRO* 3.9 22.7 - - + -
201D LEU* 3.2 30.5 - - + -
700L PHE* 3.4 22.9 - - + -
708L ARG* 5.8 1.1 - - + -
709L PRO* 3.6 21.5 - - + +
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Residues in contact with ALA 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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8D ILE* 3.8 29.6 - - + -
21D LEU* 2.6 30.1 + - + +
22D ILE* 3.7 2.9 - - - +
24D VAL* 1.3 74.8 - - - +
26D ALA* 1.3 63.8 + - - +
28D VAL* 3.0 17.0 - - - +
30D HIS* 3.0 26.7 + - + +
32D VAL* 4.1 11.0 - - + -
201D LEU* 4.5 2.9 - - + -
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Residues in contact with ALA 26 (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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22D ILE 2.8 20.7 + - - +
23D ARG 3.9 2.0 - - - +
25D ALA* 1.3 72.6 - - - +
27D ALA* 1.3 63.9 + - - +
29D GLY* 3.0 14.4 + - - -
30D HIS 3.7 14.4 + - - +
32D VAL* 4.7 3.5 - - + +
50D ILE* 3.2 35.7 - - + -
52D ASN* 4.5 12.7 - - + +
53D VAL* 4.1 10.1 - - + -
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Residues in contact with ALA 27 (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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23D ARG 3.0 18.1 + - - +
24D VAL 3.6 5.2 - - - +
25D ALA 3.3 0.2 - - - -
26D ALA* 1.3 77.7 - - - +
28D VAL* 1.3 58.3 + - + +
706L VAL* 3.3 27.4 - - + +
707L VAL 4.9 1.6 - - - +
709L PRO* 3.8 27.8 - - + -
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Residues in contact with VAL 28 (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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5D LYS* 3.2 25.6 + - - +
24D VAL 3.2 14.3 + - - +
25D ALA* 3.0 19.3 - - - +
27D ALA* 1.3 76.5 - - - +
29D GLY* 1.3 56.9 + - - +
30D HIS* 3.3 24.0 - - + +
201D LEU* 4.1 10.1 - - + -
700L PHE* 4.0 8.3 - - + -
704L HIS* 3.5 41.0 - - + +
706L VAL* 3.6 19.1 - - + +
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Residues in contact with GLY 29 (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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5D LYS* 3.2 21.4 - - - +
26D ALA 3.0 11.2 + - - -
27D ALA 3.3 0.6 - - - -
28D VAL* 1.3 80.7 - - - +
30D HIS* 1.3 63.2 + - - +
31D HIS* 4.0 11.1 + - - -
52D ASN* 5.2 5.3 - - - +
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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