Contacts of the helix formed by residues 20 - 32 (chain D) in PDB entry 5DSV
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 VAL 20 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D SER 4.6 0.2 - - - +
11D ALA* 3.7 32.8 - - - +
13D THR 4.0 7.4 - - - +
14D PHE* 3.7 30.5 - - + +
19D ARG* 1.3 71.1 - - - +
21D PHE* 1.3 67.1 + - - +
22D GLN 4.6 0.9 - - - +
23D VAL* 3.0 37.6 + - + +
24D GLU* 3.5 13.4 + - - +
123D THR 4.3 3.4 - - - +
80E LEU* 4.4 11.6 - - + +
129E ARG* 3.9 20.4 - - - +
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Residues in contact with PHE 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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2D SER* 6.0 0.9 - - - -
3D ILE* 3.7 41.1 - - + -
7D TYR 4.1 10.8 + - - -
8D ASP* 3.5 23.3 - - + -
13D THR 4.3 0.4 + - - -
15D SER* 3.4 38.1 - - - -
17D ASP* 5.2 0.2 - - - -
19D ARG* 3.3 50.6 + - + -
20D VAL* 1.3 74.5 - - - +
22D GLN* 1.3 55.2 - - - +
24D GLU* 2.8 34.2 + - - +
25D TYR* 2.9 41.2 + + + -
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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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12C SER 3.7 14.3 + - - -
13C THR* 3.7 3.6 - - - +
14C PHE* 2.5 62.9 + - - +
8D ASP* 3.2 24.3 - - - +
9D LEU 3.6 22.2 + - - -
10D SER 3.6 6.9 + - - +
11D ALA* 3.8 22.4 - - + +
20D VAL 3.2 0.2 - - - -
21D PHE* 1.3 78.4 - - - +
23D VAL* 1.3 60.0 + - - +
25D TYR* 3.9 6.9 - - - +
26D ALA* 3.3 18.0 + - - +
129D ARG* 4.2 5.1 - - - +
130D PRO* 4.0 6.1 - - + +
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Residues in contact with VAL 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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11D ALA* 5.3 0.7 - - + -
20D VAL* 3.0 29.9 + - + +
22D GLN* 1.3 75.9 - - - +
24D GLU* 1.3 68.3 + - + +
25D TYR 3.0 1.6 - - - -
26D ALA* 2.9 8.1 + - - +
27D MET* 2.9 30.2 + - + +
123D THR* 4.0 25.1 - - - +
130D PRO* 4.2 9.6 - - + -
153D PRO* 4.4 4.7 - - + +
154D SER* 3.7 39.0 - - - +
129E ARG* 5.4 0.4 - - - +
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Residues in contact with GLU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ARG* 2.5 56.0 + - - +
20D VAL 3.5 10.0 + - - +
21D PHE* 2.8 20.6 + - - +
23D VAL* 1.3 78.3 - - + +
25D TYR* 1.3 62.8 + - + +
27D MET* 3.1 27.4 + - + +
28D LYS* 3.0 32.4 + - - +
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Residues in contact with TYR 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TYR* 4.3 1.5 + + - -
14C PHE* 3.9 14.8 - - + -
15C SER 3.3 16.8 - - - +
16C PRO* 3.4 48.7 - - + +
18C GLY* 3.4 12.5 - - - -
2D SER* 5.2 3.8 - - - -
3D ILE 3.4 12.0 + - - -
8D ASP* 3.0 49.4 + - + +
21D PHE* 2.9 36.4 + + + +
22D GLN* 3.9 11.9 - - - +
24D GLU* 1.3 77.7 - - + +
26D ALA* 1.3 64.0 - - - +
28D LYS* 3.0 21.9 + - - +
29D ALA 3.1 9.0 + - - -
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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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14C PHE* 3.4 36.9 - - + -
22D GLN 3.3 8.4 + - - +
23D VAL* 2.9 12.5 + - - +
25D TYR* 1.3 77.1 - - - +
27D MET* 1.3 64.0 + - - +
29D ALA* 3.2 16.6 + - - +
30D VAL* 3.7 4.0 + - - +
130D PRO* 4.4 5.6 - - + -
131D PHE 3.6 15.5 - - - +
132D GLY* 3.9 2.9 - - - -
153D PRO* 3.9 15.3 - - + +
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Residues in contact with MET 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 VAL* 2.9 25.6 + - + +
24D GLU* 3.3 36.8 - - + +
26D ALA* 1.3 75.7 - - - +
28D LYS* 1.3 57.9 + - - +
29D ALA 3.1 0.2 - - - -
30D VAL* 2.8 29.1 + - + +
31D GLU* 3.3 9.9 + - - +
152D ASP* 4.2 22.7 - - - +
153D PRO* 4.0 24.0 - - + -
154D SER* 4.8 4.9 - - - -
169D ARG* 5.2 9.4 + - - +
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Residues in contact with LYS 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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16C PRO* 3.3 28.4 + - - +
17C ASP* 3.7 19.7 - - - +
18C GLY* 4.1 2.7 - - - -
24D GLU* 3.0 16.5 + - - +
25D TYR* 3.0 24.7 + - - +
27D MET* 1.3 74.1 - - - +
29D ALA* 1.3 60.4 + - - +
30D VAL 3.3 0.2 - - - -
31D GLU* 3.6 21.4 + - + +
32D ASN* 3.5 21.4 + - - +
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Residues in contact with ALA 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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14C PHE* 4.1 15.0 - - + -
17C ASP 5.1 0.2 - - - -
18C GLY* 3.2 26.2 - - - +
25D TYR 3.1 6.0 + - - +
26D ALA 3.3 13.5 - - - +
27D MET 3.1 0.6 - - - -
28D LYS* 1.3 76.3 - - - +
30D VAL* 1.3 62.7 + - - +
32D ASN* 3.8 5.0 + - - +
33D SER* 3.8 9.4 + - - -
79D GLY* 3.6 14.2 - - - -
80D LEU* 5.0 6.9 - - + +
132D GLY* 3.9 12.3 - - - +
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Residues in contact with VAL 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 ALA 3.9 8.3 - - - +
27D MET* 2.8 15.9 + - - +
29D ALA* 1.3 75.4 - - - +
31D GLU* 1.3 62.9 + - - +
33D SER* 3.0 21.5 + - - +
78D ALA* 3.8 24.2 - - + +
79D GLY* 3.7 5.8 - - - -
133D CYS* 3.8 11.7 - - - -
134D SER* 3.4 37.7 - - - +
153D PRO* 4.1 6.3 - - + -
166D GLY* 3.6 8.6 - - - +
169D ARG* 3.4 25.6 - - - +
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Residues in contact with GLU 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 MET* 3.3 6.0 + - - +
28D LYS* 3.7 33.4 - - + +
29D ALA 3.4 0.4 - - - -
30D VAL* 1.3 77.0 - - - +
32D ASN* 1.3 66.1 + - - +
33D SER 3.2 9.7 - - - +
166D GLY 3.6 17.6 - - - +
167D LYS* 3.2 24.5 - - - +
169D ARG* 4.0 25.8 + - - +
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Residues in contact with ASN 32 (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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17C ASP* 2.8 31.1 + - - +
18C GLY* 5.0 3.2 + - - +
19C ARG* 5.1 7.1 - - - +
28D LYS* 3.5 13.9 + - - +
29D ALA* 4.3 5.2 - - - +
30D VAL 3.2 1.0 - - - -
31D GLU* 1.3 80.3 - - - +
33D SER* 1.3 58.6 + - - +
167D LYS* 4.0 17.6 + - - +
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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