Contacts of the helix formed by residues 16 - 33 (chain O) in PDB entry 5MS0
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 ARG 16 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910D ASN* 4.6 17.8 - - + +
10O VAL* 6.4 3.4 - - + +
13O ILE 5.5 0.2 - - - -
15O ASN* 1.3 73.2 - - - +
17O PHE* 1.3 60.0 + - + +
19O LEU* 3.1 27.8 + - - +
20O VAL* 4.0 1.7 + - - +
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Residues in contact with PHE 17 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1282C GLY* 5.4 4.9 - - - +
911D LYS 5.8 4.0 - - - +
1359D ALA 5.2 2.0 - - - +
1360D GLY* 4.1 28.5 - - - +
1361D THR* 4.9 5.3 - - - +
1366D HIS* 5.6 4.9 - - + -
15O ASN* 3.5 2.0 - - + +
16O ARG* 1.3 75.2 - - + +
18O ASP* 1.3 60.1 + - - +
19O LEU 3.1 1.6 - - - -
20O VAL* 3.2 9.5 + - - +
21O LEU* 3.1 26.2 + - - +
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Residues in contact with ASP 18 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1365D TYR 6.1 0.2 - - - +
1366D HIS* 5.5 11.0 - - + +
1368D ASP* 6.5 0.9 - - + -
13O ILE* 4.8 10.5 - - + -
15O ASN* 3.8 20.4 + - + +
16O ARG 3.2 0.2 - - - -
17O PHE* 1.3 76.4 - - - +
19O LEU* 1.3 58.1 + - - +
21O LEU* 4.0 7.6 - - - +
22O VAL* 2.9 31.0 + - - +
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Residues in contact with LEU 19 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482D ALA* 6.2 3.8 - - + -
9O ALA* 4.9 20.0 - - + +
10O VAL* 6.0 1.3 - - - -
13O ILE* 5.1 6.6 - - + +
15O ASN 4.2 2.5 + - - +
16O ARG* 3.1 18.0 + - - +
18O ASP* 1.3 79.2 - - - +
20O VAL* 1.3 56.6 + - + +
22O VAL* 3.6 6.3 + - - +
23O ALA* 2.9 27.5 + - - +
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Residues in contact with VAL 20 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478D LEU* 5.2 5.9 - - + +
479D GLU* 4.8 23.8 - - + +
482D ALA* 5.5 9.6 - - + -
483D LEU* 5.8 4.7 - - + -
16O ARG 4.0 1.1 + - - +
17O PHE* 3.2 11.3 + - - +
19O LEU* 1.3 76.6 - - + +
21O LEU* 1.3 61.2 + - - +
23O ALA* 3.8 6.7 - - - +
24O ALA* 2.9 30.1 + - - +
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Residues in contact with LEU 21 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1361D THR* 4.7 17.7 - - - -
1366D HIS* 5.4 12.1 - - + +
1368D ASP 6.2 1.8 - - - +
17O PHE 3.1 16.2 + - - +
18O ASP* 4.0 7.2 - - - +
20O VAL* 1.3 77.0 - - - +
22O VAL* 1.3 58.3 + - - +
24O ALA* 4.0 3.0 - - - +
25O ARG* 2.9 32.9 + - - +
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Residues in contact with VAL 22 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1370D MET* 5.5 3.3 - - - +
18O ASP 2.9 19.9 + - - +
19O LEU* 3.6 6.5 - - - +
21O LEU* 1.3 76.3 - - - +
23O ALA* 1.3 56.3 + - - +
25O ARG* 3.9 2.8 - - - +
26O ARG* 2.9 31.6 + - - +
61O ASN* 4.9 17.7 - - + -
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Residues in contact with ALA 23 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478D LEU* 4.9 13.1 - - + +
19O LEU 2.9 19.8 + - - +
20O VAL* 4.1 6.7 - - - +
22O VAL* 1.3 76.2 - - - +
24O ALA* 1.3 58.9 + - - +
26O ARG* 3.8 5.3 - - - +
27O ALA* 2.9 30.3 + - - +
50O ALA* 4.7 7.5 - - + +
51O LEU* 6.0 7.0 - - + +
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Residues in contact with ALA 24 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474D LEU* 4.7 8.1 - - - +
475D GLU* 4.3 30.3 - - + +
478D LEU* 5.1 5.3 - - + +
20O VAL 2.9 20.2 + - - +
21O LEU* 4.0 4.5 - - - +
23O ALA* 1.3 78.5 - - - +
25O ARG* 1.3 58.0 + - - +
27O ALA* 3.5 5.5 + - - +
28O ARG* 2.9 25.9 + - - +
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Residues in contact with ARG 25 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1368D ASP 5.3 8.3 - - - +
1369D ARG* 5.6 2.0 - - - -
1370D MET* 5.2 13.2 - - + +
21O LEU 2.9 18.6 + - - +
22O VAL* 4.3 3.1 - - - +
24O ALA* 1.3 76.0 - - - +
26O ARG* 1.3 59.4 + - - +
28O ARG* 3.3 10.1 - - + +
29O GLN* 2.9 28.1 + - - +
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Residues in contact with ARG 26 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1370D MET* 4.9 13.4 - - + +
22O VAL 2.9 20.4 + - - +
23O ALA* 3.8 5.8 - - - +
25O ARG* 1.3 75.9 - - - +
27O ALA* 1.3 58.9 + - - +
29O GLN* 3.6 4.8 + - - +
30O MET* 2.9 28.8 + - - +
50O ALA* 4.6 13.1 - - + +
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Residues in contact with ALA 27 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474D LEU* 5.2 17.9 - - + +
23O ALA 2.9 17.8 + - - +
24O ALA* 3.9 5.4 - - - +
26O ARG* 1.3 73.5 - - - +
28O ARG* 1.3 60.5 + - - +
30O MET* 3.6 8.4 - - - +
31O GLN* 2.9 30.5 + - - +
50O ALA* 4.4 12.7 - - + +
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Residues in contact with ARG 28 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474D LEU* 6.4 0.7 - - - -
24O ALA 2.9 15.2 + - - +
25O ARG* 3.3 14.6 - - - +
26O ARG 3.2 0.2 - - - -
27O ALA* 1.3 77.4 - - - +
29O GLN* 1.3 57.5 + - - +
31O GLN* 3.4 2.2 + - - +
32O VAL* 2.9 34.7 + - - +
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Residues in contact with GLN 29 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1370D MET* 5.7 6.5 - - + -
25O ARG 2.9 16.6 + - - +
26O ARG* 4.2 4.5 - - - +
28O ARG* 1.3 75.6 - - - +
30O MET* 1.3 57.2 + - - +
32O VAL* 5.0 0.9 - - - -
33O GLY* 3.0 28.5 + - - +
34O GLY 3.7 3.1 + - - -
35O LYS 5.4 1.4 - - - +
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Residues in contact with MET 30 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26O ARG 2.9 19.6 + - - +
27O ALA* 3.8 9.6 - - - +
28O ARG 3.2 0.2 - - - -
29O GLN* 1.3 79.6 - - - +
31O GLN* 1.3 59.1 + - - +
34O GLY 2.8 27.7 - - - +
35O LYS* 4.8 9.5 - - - -
36O ASP* 5.8 4.9 - - + +
50O ALA* 5.3 6.7 - - + -
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Residues in contact with GLN 31 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1311C GLY 5.6 5.6 - - - +
1312C ASN* 5.9 4.9 - - - -
1313C HIS 6.1 0.9 - - - +
27O ALA 2.9 17.9 + - - +
28O ARG* 4.1 2.0 - - - +
30O MET* 1.3 78.8 - - - +
32O VAL* 1.3 64.1 + - - +
34O GLY* 4.7 2.1 + - - +
89O GLY* 5.7 3.1 - - - -
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Residues in contact with VAL 32 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28O ARG 2.9 15.8 + - - +
29O GLN* 5.0 1.3 - - - -
31O GLN* 1.3 78.1 - - + +
33O GLY* 1.3 67.0 + - - +
34O GLY 3.7 0.2 + - - -
87O ALA 4.6 1.9 - - - +
88O GLU 4.8 0.7 - - - -
89O GLY* 4.2 20.1 + - - -
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Residues in contact with GLY 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29O GLN* 3.0 19.5 + - - +
32O VAL* 1.3 80.6 - - - +
34O GLY* 1.3 56.5 + - - +
81O GLN* 4.8 9.5 - - - +
85O ALA* 3.3 19.7 - - - +
87O ALA 3.2 18.3 - - - +
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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
------------------------------------------------------------
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