Contacts of the helix formed by residues 13 - 31 (chain D) in PDB entry 2HVY
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 PRO 13 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLU* 3.7 7.9 - - + +
12D VAL* 1.4 93.9 - - + +
14D LYS* 1.3 65.6 + - - +
15D GLU* 3.2 14.1 - - + +
16D LEU* 3.2 17.6 + - + +
17D ALA* 3.2 19.5 + - - +
122D LEU* 4.0 20.4 - - + -
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Residues in contact with LYS 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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12D VAL 3.8 1.4 + - - -
13D PRO* 1.3 72.7 - - - +
15D GLU* 1.3 74.6 + - - +
17D ALA* 3.7 7.3 + - - +
18D GLU* 3.4 27.2 + - + +
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Residues in contact with GLU 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D PRO* 4.1 9.1 - - + +
14D LYS* 1.3 95.1 + - - +
16D LEU* 1.3 58.8 + - - +
18D GLU* 3.4 8.6 + - - +
19D LYS* 3.1 38.5 + - - +
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Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D VAL* 4.3 2.0 - - + -
13D PRO* 3.2 23.4 + - + +
15D GLU* 1.3 76.2 - - - +
17D ALA* 1.3 60.6 + - - +
19D LYS* 3.4 15.4 + - + +
20D ALA* 3.1 26.5 + - - +
79D ILE* 3.8 24.3 - - + +
114D GLU 5.4 0.4 - - - -
115D ILE* 4.5 20.6 - - + +
118D LYS* 3.8 38.4 - - + +
119D VAL* 4.2 9.0 - - + -
122D LEU* 3.8 26.0 - - + -
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Residues in contact with ALA 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D VAL* 4.0 15.6 - - + +
13D PRO 3.2 16.3 + - - +
14D LYS* 3.9 7.9 - - - +
15D GLU 3.3 0.2 - - - -
16D LEU* 1.3 74.1 - - - +
18D GLU* 1.3 57.8 + - - +
20D ALA* 3.4 4.9 + - - +
21D LEU* 3.1 35.0 + - + +
79D ILE* 5.3 0.2 - - - -
80D TYR 4.1 4.3 - - - +
81D VAL* 3.6 6.9 - - + +
82D PRO* 4.0 27.1 - - + -
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Residues in contact with GLU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LYS* 3.4 16.7 + - + +
15D GLU* 3.4 11.8 + - - +
16D LEU 3.3 0.2 - - - -
17D ALA* 1.3 75.9 - - - +
19D LYS* 1.3 58.5 + - + +
21D LEU* 3.2 19.8 + - + +
22D GLN* 2.8 46.3 + - - +
86D GLU* 4.8 5.8 - - - +
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Residues in contact with LYS 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 GLU* 3.1 20.1 + - - +
16D LEU* 3.6 21.8 - - + +
17D ALA 3.4 0.2 - - - -
18D GLU* 1.3 76.2 - - + +
20D ALA* 1.3 57.8 + - - +
22D GLN* 3.9 18.0 - - - +
23D ALA* 3.0 27.9 + - - +
111D LEU* 3.5 20.1 - - + +
114D GLU* 3.6 38.0 + - - +
115D ILE* 3.6 12.0 - - + +
118D LYS* 4.9 5.6 - - - +
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Residues in contact with ALA 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 LEU 3.1 13.9 + - - +
17D ALA 3.6 8.7 - - - +
18D GLU 3.2 0.2 - - - -
19D LYS* 1.3 74.6 - - - +
21D LEU* 1.3 60.3 + - - +
23D ALA* 3.2 4.0 + - - +
24D VAL* 3.1 31.2 + - - +
51D LEU* 5.4 0.7 - - + -
53D ILE* 4.5 6.7 - - + +
79D ILE* 3.9 34.3 - - + -
81D VAL* 4.2 9.4 - - + -
115D ILE* 3.7 13.4 - - + +
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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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17D ALA* 3.1 21.9 + - + +
18D GLU* 3.2 23.3 + - + +
20D ALA* 1.3 73.2 - - - +
22D GLN* 1.3 60.6 + - - +
24D VAL* 3.4 6.4 + - - +
25D GLU* 3.1 26.7 + - - +
81D VAL* 3.9 17.0 - - + -
82D PRO* 5.2 4.9 - - + -
83D SER 5.3 0.2 - - - +
86D GLU* 3.9 37.0 - - + +
87D LEU* 3.8 43.7 - - + +
90D ALA* 3.8 11.1 - - + +
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Residues in contact with GLN 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 GLU* 2.8 30.9 + - - +
19D LYS* 3.6 26.8 - - - +
21D LEU* 1.3 76.6 - - - +
23D ALA* 1.3 56.5 + - - +
25D GLU* 3.3 7.1 + - - +
26D ILE* 3.0 39.9 + - + +
111D LEU* 3.8 18.0 - - + +
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Residues in contact with ALA 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 LYS 3.0 18.8 + - - +
20D ALA* 3.2 7.4 + - - +
22D GLN* 1.3 73.9 - - - +
24D VAL* 1.3 61.5 + - - +
27D ALA* 3.2 27.4 + - - +
51D LEU* 4.9 0.2 - - + -
102D ILE* 4.0 18.0 - - + +
108D ALA* 4.0 8.5 - - + +
111D LEU* 3.6 16.1 - - + +
112D VAL* 4.4 9.4 - - + -
115D ILE* 3.9 15.3 - - + -
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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 ALA 3.1 16.6 + - - +
21D LEU* 3.7 7.0 - - - +
22D GLN 3.3 0.2 - - - -
23D ALA* 1.3 75.9 - - - +
25D GLU* 1.3 64.6 + - - +
27D ALA* 3.6 1.6 + - - +
28D ARG* 3.1 27.4 + - - +
33D ILE* 4.6 6.6 - - + +
53D ILE* 3.7 30.1 - - + -
87D LEU* 4.3 14.4 - - + +
90D ALA* 3.5 28.3 - - + +
91D ALA* 3.8 10.8 - - + +
100D VAL* 4.0 21.1 - - + -
102D ILE* 4.6 4.9 - - + -
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Residues in contact with GLU 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 LEU 3.1 13.9 + - - +
22D GLN* 3.3 12.3 + - - +
24D VAL* 1.3 77.6 - - - +
26D ILE* 1.3 62.3 + - + +
28D ARG* 2.9 47.7 + - - +
29D ASP* 2.9 22.3 - - - +
89D ALA 4.4 0.9 - - - +
90D ALA* 3.6 19.0 + - + +
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Residues in contact with ILE 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 GLN* 3.0 26.7 + - + +
25D GLU* 1.3 78.9 - - + +
27D ALA* 1.3 60.7 + - - +
28D ARG 3.1 2.1 + - - -
29D ASP* 3.4 10.7 + - - +
30D THR* 2.7 42.0 + - + +
107D LYS* 3.8 24.9 - - + -
108D ALA* 3.8 21.5 - - + +
111D LEU* 4.2 9.9 - - + -
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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 ALA 3.2 20.8 + - - +
24D VAL 4.2 0.2 - - - +
26D ILE* 1.3 76.2 - - - +
28D ARG* 1.3 60.1 + - - +
29D ASP 3.3 0.2 - - - -
30D THR* 3.7 2.0 - - - -
31D GLY 2.9 31.6 + - - +
32D LYS* 3.3 2.8 + - - -
33D ILE* 3.8 19.3 - - + -
102D ILE* 4.2 4.5 - - + -
104D GLU 3.8 8.3 - - - +
105D PRO* 3.3 30.0 + - + +
108D ALA* 4.9 0.4 - - + -
112D VAL* 6.2 0.2 - - + -
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Residues in contact with ARG 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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24D VAL 3.1 19.3 + - - +
25D GLU* 2.9 42.7 + - - +
26D ILE 3.1 0.4 - - - -
27D ALA* 1.3 79.0 - - - +
29D ASP* 1.3 80.9 + - - +
31D GLY 4.2 6.8 - - - +
32D LYS* 5.4 1.0 - - - -
33D ILE* 3.8 20.4 - - + +
89D ALA 3.6 13.1 + - - -
90D ALA 3.5 8.3 + - - +
91D ALA 3.4 28.3 - - - +
92D GLY* 3.6 11.2 - - - -
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Residues in contact with ASP 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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25D GLU* 2.9 19.9 - - - +
26D ILE* 3.4 12.4 - - - +
28D ARG* 1.3 99.0 + - + +
30D THR* 1.3 70.1 + - - +
31D GLY 3.8 1.1 - - - -
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Residues in contact with THR 30 (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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26D ILE* 2.7 26.4 + - + +
27D ALA* 3.7 2.4 - - - -
29D ASP* 1.3 95.8 - - - +
31D GLY* 1.3 58.7 + - - +
105D PRO 3.8 0.3 + - - -
106D GLY* 4.4 6.7 - - - -
107D LYS* 3.5 53.6 + - + -
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Residues in contact with GLY 31 (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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27D ALA 2.9 12.7 + - - +
28D ARG 4.2 6.8 - - - +
29D ASP 5.0 0.7 - - - -
30D THR* 1.3 82.6 + - - +
32D LYS* 1.3 63.1 + - - +
104D GLU* 3.4 19.5 - - - -
106D GLY* 4.6 4.7 - - - -
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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
------------------------------------------------------------
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