Contacts of the helix formed by residues 13 - 33 (chain A) in PDB entry 3N4H
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 SER 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ILE 5.0 1.3 + - - -
11A ARG 3.9 3.0 + - - -
12A ILE* 1.3 78.7 - - - +
14A ARG* 1.3 65.7 + - - +
15A GLU* 3.6 8.6 + - - +
16A ALA* 3.0 27.2 + - - +
17A LYS* 3.0 21.5 + - - +
93A LEU* 5.6 0.2 - - - +
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Residues in contact with ARG 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A SER* 1.3 73.8 - - - +
15A GLU* 1.3 62.6 + - - +
17A LYS* 3.5 12.9 + - - +
18A GLN* 3.3 19.8 + - - +
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Residues in contact with GLU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A SER* 3.6 7.7 + - - +
14A ARG* 1.3 82.7 - - - +
16A ALA* 1.3 61.8 + - - +
18A GLN* 3.3 9.3 + - + +
19A ARG* 3.2 52.5 + - + +
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 3.7 19.7 - - + -
13A SER* 3.0 20.8 + - - +
15A GLU* 1.3 75.4 + - - +
17A LYS* 1.3 55.8 + - - +
19A ARG* 3.4 14.4 + - - +
20A ILE* 2.8 39.5 + - - +
92A ILE* 4.1 10.5 - - + +
93A LEU* 4.1 15.9 - - + -
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Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A SER* 5.9 0.7 - - - -
12A ILE* 3.6 32.2 + - + -
13A SER 3.0 16.5 + - - +
14A ARG* 3.6 14.3 - - - +
15A GLU 3.3 0.2 - - - -
16A ALA* 1.3 73.6 - - - +
18A GLN* 1.3 63.6 + - - +
21A ALA* 2.9 21.7 + - - +
43A PHE* 3.3 61.0 + - + +
45A GLU* 3.6 26.8 + - - +
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Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ARG 3.3 9.5 + - - +
15A GLU* 3.3 13.3 + - + +
17A LYS* 1.3 79.0 - - - +
19A ARG* 1.3 56.9 + - + +
21A ALA* 3.4 5.2 + - - +
22A GLU* 3.0 29.3 + - - +
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Residues in contact with ARG 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLU* 3.2 42.1 + - + +
16A ALA* 3.7 11.4 - - - +
18A GLN* 1.3 76.5 - - + +
20A ILE* 1.3 60.2 + - - +
22A GLU* 3.5 6.9 + - - +
23A ALA* 2.9 23.7 + - - +
91A LEU 5.1 1.2 + - - -
92A ILE* 3.6 62.5 + - + +
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Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A CYS* 4.6 2.2 - - - -
12A ILE* 3.9 31.9 - - + -
16A ALA 2.8 24.5 + - - +
19A ARG* 1.3 70.3 - - - +
21A ALA* 1.3 59.6 + - - +
23A ALA* 3.2 2.6 + - - +
24A ILE* 2.8 49.4 + - + +
43A PHE* 3.6 20.2 - - + -
89A ILE* 4.0 24.5 - - + -
92A ILE* 4.0 23.1 - - + -
93A LEU* 4.1 24.7 - - + -
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LYS 2.9 18.6 + - - +
18A GLN* 3.8 5.6 - - - +
20A ILE* 1.3 75.8 - - - +
22A GLU* 1.3 58.5 + - - +
24A ILE* 3.8 0.7 - - - +
25A THR* 2.8 38.3 + - - +
41A VAL* 4.1 33.2 - - + -
43A PHE* 4.1 3.1 - - + -
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Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLN 3.0 17.6 + - - +
19A ARG* 3.6 8.1 - - - +
21A ALA* 1.3 77.1 - - - +
23A ALA* 1.3 62.0 + - - +
25A THR* 3.4 5.1 + - - -
26A ASP* 3.0 35.5 + - - +
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ARG 2.9 17.2 + - - +
20A ILE* 3.2 4.7 + - - +
22A GLU* 1.3 77.0 - - - +
24A ILE* 1.3 57.6 + - + +
26A ASP* 3.8 5.2 - - - +
27A ALA* 2.8 31.8 + - - +
85A LEU* 5.0 2.0 - - + -
88A GLU* 3.2 33.0 - - + +
89A ILE* 5.6 2.9 - - + +
92A ILE* 4.1 17.0 - - + -
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Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A TYR* 3.4 48.5 - - + -
5A CYS* 3.7 22.7 - - - -
20A ILE* 2.8 43.2 + - + +
21A ALA 3.9 2.7 - - - +
23A ALA* 1.3 73.5 - - + +
25A THR* 1.3 58.1 + - - +
27A ALA* 3.4 1.7 + - - +
28A HIS* 3.0 28.8 + - - +
39A VAL* 4.3 1.6 - - + -
41A VAL* 3.9 19.7 - - + -
65A VAL* 4.7 2.7 - - + -
85A LEU* 3.8 21.4 - - + +
89A ILE* 4.4 12.1 - - + -
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Residues in contact with THR 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA* 2.8 28.4 + - - +
22A GLU* 3.8 5.8 - - - -
24A ILE* 1.3 72.4 - - - +
26A ASP* 1.3 57.4 + - - +
28A HIS* 3.4 1.0 + - - +
29A HIS* 3.0 31.9 + - - +
36A LYS* 3.7 44.9 - - + +
39A VAL* 3.7 25.9 + - + +
41A VAL* 4.2 4.9 - - - +
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Residues in contact with ASP 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLU* 3.0 27.1 + - - +
23A ALA* 3.8 5.5 - - - +
25A THR* 1.3 71.9 - - - +
27A ALA* 1.4 66.6 + - - +
28A HIS 3.1 0.9 - - - -
29A HIS* 3.4 4.4 + - - +
30A GLU* 3.1 42.5 + - - +
36A LYS* 3.1 31.2 + - - +
84A ARG* 3.9 10.1 - - - +
88A GLU* 5.7 0.7 - - - +
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA 2.8 21.2 + - - +
24A ILE 3.7 0.4 - - - +
26A ASP* 1.4 73.3 - - - +
28A HIS* 1.3 65.6 + - - +
31A LEU* 3.0 29.3 + - + +
81A LEU* 3.8 10.4 - - + +
84A ARG* 3.6 35.7 - - + +
85A LEU* 3.7 26.0 - - + -
88A GLU* 5.2 0.4 - - - +
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Residues in contact with HIS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A PR7 3.3 65.5 + - + +
3A TYR* 2.7 31.1 + - + +
24A ILE 3.0 17.7 + - - +
25A THR 4.0 2.2 - - - +
27A ALA* 1.3 78.0 - - - +
29A HIS* 1.3 68.3 + - - +
32A ALA* 2.9 43.7 + - + +
33A HIS 3.7 0.3 + - - -
34A ALA* 3.9 11.6 - - + +
39A VAL* 4.0 10.1 - - + -
69A ILE* 3.9 10.5 - - + -
73A ARG* 4.4 0.2 - - - -
81A LEU* 4.1 10.7 - - + +
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Residues in contact with HIS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A THR 3.0 17.5 + - - +
26A ASP* 3.7 3.8 - - - +
28A HIS* 1.3 80.8 - - - +
30A GLU* 1.3 75.5 + - + +
33A HIS* 3.2 17.3 + - - -
34A ALA 2.7 40.8 + - - +
35A PRO* 4.4 7.4 - - + -
36A LYS* 3.4 41.0 + - + +
39A VAL* 5.0 0.8 - - - +
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Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ASP* 3.1 30.1 + - - +
29A HIS* 1.3 92.6 - - + +
31A LEU* 1.3 63.4 + - + +
33A HIS* 3.5 23.9 + - - -
84A ARG* 2.4 42.0 + - - +
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA 3.0 16.5 + - - +
30A GLU* 1.3 80.4 - - + +
32A ALA* 1.3 60.3 + - - +
33A HIS* 3.4 4.9 + - - -
77A GLN* 3.1 41.8 - - + +
80A GLU* 3.8 27.8 - - + +
81A LEU* 3.6 39.0 - - + +
84A ARG* 3.8 37.9 - - + +
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Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A HIS* 2.9 45.4 + - + +
31A LEU* 1.3 77.0 - - - +
33A HIS* 1.3 74.5 + - - +
69A ILE* 5.5 0.4 - - + -
73A ARG* 3.2 39.1 + - + +
77A GLN* 4.1 3.7 - - - +
81A LEU* 4.9 8.5 - - + -
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Residues in contact with HIS 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A HIS 3.7 0.2 + - - -
29A HIS 3.2 13.2 + - - -
30A GLU* 3.5 16.5 + - - -
31A LEU* 3.4 8.7 - - - -
32A ALA* 1.3 79.7 - - - +
34A ALA* 1.3 61.0 + - - +
73A ARG* 4.4 1.7 + - - -
76A LYS* 6.1 0.9 - - - -
77A GLN* 3.2 30.1 + - + -
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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