Contacts of the helix formed by residues 18 - 33 (chain E) in PDB entry 5NSS
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 ASP 18 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1361D THR 3.7 8.1 - - - +
1364D ALA* 3.2 34.7 + - - +
15E ASN* 3.0 22.8 + - - +
17E PHE* 1.3 83.2 - - - +
19E LEU* 1.3 59.6 + - - +
20E VAL 3.0 2.9 - - - -
21E LEU* 2.9 31.5 + - + +
22E VAL* 2.9 23.5 + - + +
61E ASN* 5.8 2.0 - - - +
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Residues in contact with LEU 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482D ALA* 3.7 27.1 - - + -
6E VAL* 3.9 24.9 - - + -
9E ALA* 4.4 18.6 - - + +
10E VAL* 4.8 9.4 - - + -
13E ILE 5.0 7.4 - - - +
15E ASN* 4.3 5.2 - - + +
16E ARG* 4.3 23.0 - - - +
17E PHE 3.5 1.4 - - - -
18E ASP* 1.3 77.5 - - - +
20E VAL* 1.3 57.2 + - + +
22E VAL* 3.8 8.3 - - + +
23E ALA* 2.9 40.1 + - + +
51E LEU* 5.7 5.2 - - + -
54E ILE* 4.9 13.2 - - + -
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Residues in contact with VAL 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1285C TYR* 4.4 13.2 - - + -
475D GLU* 4.1 13.7 - - - +
478D LEU* 3.4 11.3 - - + +
479D GLU* 3.6 47.3 - - + +
482D ALA* 4.5 5.2 - - + -
483D LEU* 3.9 23.8 - - + -
1361D THR* 4.2 14.4 - - + -
16E ARG 4.9 3.1 - - - +
17E PHE 4.5 3.8 - - - +
18E ASP 3.0 0.4 - - - -
19E LEU* 1.3 78.2 - - + +
21E LEU* 1.3 50.4 + - - +
24E ALA* 2.6 40.3 + - + +
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Residues in contact with LEU 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1285C TYR* 4.3 19.1 - - - +
1361D THR 6.0 1.8 - - - +
1364D ALA* 6.1 3.8 - - + -
1365D TYR* 5.7 9.9 - - + -
18E ASP* 2.9 21.8 + - + +
20E VAL* 1.3 78.0 - - - +
22E VAL* 1.3 67.3 + - + +
24E ALA* 3.7 4.3 - - - +
25E ARG* 2.9 33.3 + - + +
61E ASN* 6.0 1.1 - - - +
64E LEU* 6.5 0.4 - - + -
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Residues in contact with VAL 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E ASP* 2.9 27.4 + - + +
19E LEU* 4.1 7.4 - - + +
21E LEU* 1.3 79.0 - - + +
23E ALA* 1.3 60.9 + - - +
25E ARG* 2.9 9.1 + - - +
26E ARG* 2.9 27.0 + - - +
54E ILE* 3.8 24.5 - - + -
60E ASN* 4.8 9.9 - - - -
61E ASN* 3.3 30.7 - - - +
64E LEU* 3.7 20.3 - - + +
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Residues in contact with ALA 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478D LEU* 3.3 20.8 - - + +
19E LEU* 2.9 29.8 + - + +
22E VAL* 1.3 77.9 - - - +
24E ALA* 1.3 55.9 + - - +
26E ARG* 4.5 2.9 - - - +
27E ALA* 2.9 31.7 + - - +
50E ALA* 3.9 5.7 - - + +
51E LEU* 4.4 13.5 - - + -
54E ILE* 4.5 18.8 - - + +
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Residues in contact with ALA 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474D LEU* 3.3 38.9 - - + +
475D GLU* 5.0 0.4 - - - +
478D LEU* 3.4 13.4 - - + +
20E VAL* 2.6 27.5 + - + +
21E LEU* 4.0 5.2 - - - +
23E ALA* 1.3 75.6 - - - +
25E ARG* 1.3 58.9 + - - +
28E ARG* 2.8 28.0 + - - +
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Residues in contact with ARG 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E LEU* 2.9 24.7 + - + +
22E VAL 2.9 5.8 + - - +
24E ALA* 1.3 76.3 - - - +
26E ARG* 1.3 59.5 + - - +
28E ARG* 3.2 6.9 + - - +
29E GLN* 2.9 36.1 + - + +
64E LEU* 4.1 17.3 - - + -
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Residues in contact with ARG 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E VAL 2.9 13.6 + - - +
23E ALA* 4.0 2.5 - - - +
25E ARG* 1.3 78.1 - - - +
27E ALA* 1.3 57.9 + - - +
29E GLN* 3.0 28.4 + - - +
30E MET* 2.9 56.2 + - + +
35E LYS* 3.8 16.8 - - - +
36E ASP 3.2 25.3 + - - -
38E LEU* 3.4 21.8 - - - +
50E ALA* 3.7 16.2 - - + +
53E GLU* 4.6 15.2 - - + +
54E ILE* 5.2 1.8 - - + -
59E ILE* 4.8 30.7 - - + +
64E LEU* 4.9 6.4 - - + +
67E ARG* 4.4 19.4 - - - +
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Residues in contact with ALA 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474D LEU* 4.3 7.0 - - + +
478D LEU* 4.1 9.2 - - + -
23E ALA 2.9 19.9 + - - +
24E ALA* 4.4 2.0 - - - +
26E ARG* 1.3 75.9 - - - +
28E ARG* 1.3 49.2 + - - +
30E MET* 4.5 2.7 - - - +
31E GLN* 2.7 40.8 + - - +
46E THR* 4.2 5.5 + - - -
47E THR* 3.8 35.9 - - - +
50E ALA* 3.7 8.1 - - + +
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Residues in contact with ARG 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1312C ASN 5.9 0.4 - - - +
1313C HIS* 6.0 0.2 - - + -
474D LEU* 3.6 22.7 - - + -
24E ALA 2.8 23.3 + - - +
25E ARG* 3.4 8.5 - - - +
26E ARG 3.0 0.4 - - - -
27E ALA* 1.3 76.6 - - - +
29E GLN* 1.3 61.1 + - + +
31E GLN* 4.3 2.5 - - - -
32E VAL* 2.9 42.1 + - + +
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Residues in contact with GLN 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ARG* 2.9 20.3 + - - +
26E ARG* 3.0 31.2 + - - +
28E ARG* 1.3 76.5 - - + +
30E MET* 1.3 59.8 + - - +
32E VAL* 5.2 0.7 - - - -
33E GLY 3.1 29.2 + - - +
34E GLY 4.4 0.2 - - - -
35E LYS* 3.6 16.8 - - + +
64E LEU* 4.2 20.8 + - - +
67E ARG* 5.0 11.1 + - - +
68E GLU* 5.1 16.2 - - - +
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Residues in contact with MET 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ARG* 2.9 57.6 + - + +
27E ALA 4.5 0.4 - - - +
29E GLN* 1.3 74.0 - - - +
31E GLN* 1.3 64.1 + - - +
33E GLY* 3.7 8.2 + - - -
35E LYS* 3.7 33.3 - - + +
36E ASP 4.6 0.2 - - - -
37E PRO* 4.0 24.7 - - + -
38E LEU 5.3 0.2 - - - -
46E THR* 3.3 51.2 - - + +
49E ILE* 4.1 10.3 - - + +
50E ALA* 3.7 14.4 - - + +
53E GLU* 5.3 0.7 - - + -
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Residues in contact with GLN 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1310C ASP 4.5 3.8 - - - +
1311C GLY* 4.8 12.7 - - - +
1313C HIS* 6.2 2.7 - - + -
387D LEU* 5.5 11.1 - - - +
474D LEU* 5.4 6.1 - - + -
27E ALA 2.7 23.0 + - - +
28E ARG* 4.1 3.6 - - - +
30E MET* 1.3 78.5 - - - +
32E VAL* 1.3 64.7 + - + +
33E GLY* 3.4 0.3 + - - -
45E LYS* 4.6 19.8 - - - +
46E THR* 3.5 19.7 + - - +
47E THR* 4.7 8.1 + - - -
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Residues in contact with VAL 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1310C ASP* 3.9 22.5 - - + +
1311C GLY 3.2 24.5 - - - +
1312C ASN* 4.4 13.7 - - - +
1313C HIS* 5.8 0.9 - - + -
28E ARG* 2.9 28.3 + - + +
29E GLN* 4.7 0.7 - - - +
31E GLN* 1.3 77.7 - - + +
33E GLY* 1.3 63.3 + - - +
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Residues in contact with GLY 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E GLN* 3.1 17.4 + - - +
30E MET 3.7 6.9 + - - -
31E GLN 3.2 4.2 - - - -
32E VAL* 1.3 87.0 - - - +
34E GLY* 1.3 60.7 + - - -
35E LYS 3.5 1.8 - - - -
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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