Contacts of the helix formed by residues 20 - 32 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M SER 4.6 0.7 - - - +
11M ALA* 3.7 32.8 - - - +
13M THR 4.0 6.3 - - - +
14M PHE* 3.6 31.0 - - + +
19M ARG* 1.3 70.2 - - - +
21M PHE* 1.3 66.2 + - - +
22M GLN 4.6 0.2 - - - +
23M VAL* 3.0 36.1 + - + +
24M GLU* 3.5 13.7 + - - +
123M THR 4.3 3.6 - - - +
80N LEU* 4.5 10.7 - - + +
129N ARG* 3.9 21.1 - - - +
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Residues in contact with PHE 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1M SER* 4.1 10.1 - - - -
3M ILE* 3.6 40.2 - - + -
7M TYR 3.9 11.4 + - - +
8M ASP* 3.5 22.2 - - + -
13M THR 4.3 0.6 + - - -
15M SER* 3.4 35.9 - - - -
17M ASP* 4.7 0.2 - - - -
19M ARG* 3.3 50.0 + - + -
20M VAL* 1.3 73.3 - - - +
22M GLN* 1.3 56.8 + - - +
24M GLU* 2.9 32.3 + - - +
25M TYR* 2.9 43.1 + + + -
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Residues in contact with GLN 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L SER 3.6 14.6 + - - -
13L THR* 3.7 3.4 - - - +
14L PHE* 2.6 62.7 + - - +
8M ASP* 3.2 24.3 - - - +
9M LEU 3.5 22.7 - - - -
10M SER 3.6 7.4 + - - +
11M ALA* 3.7 24.0 - - + +
20M VAL* 5.0 0.2 - - + -
21M PHE* 1.3 79.6 - - - +
23M VAL* 1.3 57.6 + - - +
25M TYR* 3.9 7.9 - - - +
26M ALA* 3.3 18.5 + - - +
129M ARG* 4.2 4.9 - - - +
130M PRO* 4.0 6.5 - - + +
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Residues in contact with VAL 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M ALA* 5.3 0.7 - - + -
20M VAL* 3.0 30.7 + - + +
22M GLN* 1.3 73.2 - - - +
24M GLU* 1.3 69.6 + - + +
25M TYR 3.0 1.6 - - - -
26M ALA* 2.9 7.7 + - + +
27M MET* 2.9 30.0 + - + +
123M THR* 4.0 25.4 - - + +
130M PRO* 4.2 10.1 - - + -
153M PRO* 4.4 5.2 - - + +
154M SER* 3.7 39.5 - - - +
129N ARG* 5.4 0.4 - - - +
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Residues in contact with GLU 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M ARG* 2.5 54.8 + - - +
20M VAL 3.5 9.7 + - - +
21M PHE* 2.9 20.7 + - - +
23M VAL* 1.3 77.0 - - + +
25M TYR* 1.3 62.7 + - + +
27M MET* 3.1 28.7 + - + +
28M LYS* 3.0 32.3 + - - +
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Residues in contact with TYR 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L TYR* 4.3 1.7 + + - -
14L PHE* 3.8 15.9 - - + -
15L SER 3.4 16.6 - - - +
16L PRO* 3.4 50.5 - - + +
18L GLY* 3.4 13.1 - - - -
2M SER* 5.2 3.8 - - - -
3M ILE 3.4 11.6 + - - -
8M ASP* 3.0 48.3 + - + +
21M PHE* 2.9 35.8 + + + +
22M GLN* 3.9 13.7 - - - +
24M GLU* 1.3 78.6 - - + +
26M ALA* 1.3 59.6 + - - +
28M LYS* 3.0 25.0 + - - +
29M ALA 3.1 9.0 + - - -
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Residues in contact with ALA 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14L PHE* 3.4 33.6 - - + -
22M GLN 3.3 9.5 + - - +
23M VAL* 2.9 12.5 + - - +
25M TYR* 1.3 76.8 - - - +
27M MET* 1.3 64.5 + - - +
29M ALA* 3.2 16.8 + - - +
30M VAL* 3.7 3.6 + - - +
130M PRO* 4.4 5.6 - - + -
131M PHE 3.6 16.4 - - - +
132M GLY* 4.0 3.1 - - - -
153M PRO* 3.9 15.5 - - + +
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Residues in contact with MET 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23M VAL* 2.9 25.0 + - + +
24M GLU* 3.1 38.5 + - + +
26M ALA* 1.3 77.5 - - - +
28M LYS* 1.3 56.5 + - - +
30M VAL* 2.8 29.7 + - + +
31M GLU* 3.3 9.5 + - + +
152M ASP* 4.2 22.2 - - - +
153M PRO* 4.0 23.3 - - + -
154M SER* 4.8 5.2 - - - -
169M ARG* 5.2 9.2 + - - +
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Residues in contact with LYS 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L PRO* 3.2 28.8 + - - +
17L ASP* 3.6 13.6 - - + +
18L GLY* 4.0 2.5 - - - -
24M GLU* 3.0 16.9 + - - +
25M TYR* 3.0 25.8 + - - +
27M MET* 1.3 71.6 - - - +
29M ALA* 1.3 61.9 + - - +
30M VAL 3.2 0.2 - - - -
31M GLU* 3.7 21.6 - - + +
32M ASN* 3.5 28.6 + - - +
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Residues in contact with ALA 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14L PHE* 4.0 15.0 - - + -
18L GLY* 3.2 27.1 - - - +
25M TYR 3.1 5.1 + - - -
26M ALA 3.3 13.5 - - - +
27M MET 3.1 0.2 - - - -
28M LYS* 1.3 77.3 - - - +
30M VAL* 1.3 63.5 + - - +
32M ASN* 3.8 4.7 + - - +
33M SER* 3.8 9.4 + - - -
79M GLY* 3.7 12.8 - - - -
80M LEU* 5.0 6.7 - - + +
132M GLY* 3.9 12.3 - - - +
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Residues in contact with VAL 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26M ALA 3.9 7.6 - - - +
27M MET* 2.8 16.3 + - - +
29M ALA* 1.3 75.2 - - - +
31M GLU* 1.3 64.0 + - - +
33M SER* 3.0 21.8 + - - +
78M ALA* 3.8 23.8 - - + +
79M GLY* 3.8 5.8 - - - -
132M GLY 4.2 0.2 - - - +
133M CYS* 3.8 11.9 - - - -
134M SER* 3.4 36.6 - - - +
153M PRO* 4.1 7.0 - - + -
165M ILE* 4.6 0.4 - - + -
166M GLY* 3.5 7.2 - - - +
169M ARG* 3.4 26.0 - - - +
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Residues in contact with GLU 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M MET* 3.8 6.1 - - + +
28M LYS* 3.7 33.9 - - + +
29M ALA 3.4 0.4 - - - -
30M VAL* 1.3 77.5 - - - +
32M ASN* 1.3 65.5 + - - +
33M SER 3.2 9.9 - - - +
166M GLY 3.6 17.5 - - - +
167M LYS* 3.2 23.3 - - - +
169M ARG* 4.0 25.5 + - - +
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Residues in contact with ASN 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L ASP* 2.8 30.3 + - - +
18L GLY 4.9 4.0 + - - +
19L ARG* 4.9 8.5 - - - +
28M LYS* 3.5 12.8 + - - +
29M ALA* 4.3 5.8 - - - +
30M VAL 3.2 0.8 - - - -
31M GLU* 1.3 81.3 - - - +
33M SER* 1.3 58.3 + - - +
167M 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
------------------------------------------------------------
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