Contacts of the helix formed by residues 16 - 34 (chain A) in PDB entry 2V1N
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 MET 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PRO 4.3 2.9 + - - -
13A GLN 4.5 4.5 - - - +
14A GLN 3.4 2.2 - - - -
15A PHE* 1.4 73.4 - - - +
17A ASP* 1.4 58.4 + - - +
19A PHE* 5.2 1.1 - - - -
20A SER* 2.9 56.8 + - - +
61A THR* 4.9 4.0 - - - +
62A GLN* 3.6 57.9 - - + +
63A TRP* 3.2 41.7 - - + +
72A TRP* 3.7 21.8 - - + +
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Residues in contact with ASP 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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14A GLN 5.1 3.7 + - - +
15A PHE* 3.4 1.5 - - - +
16A MET* 1.4 76.7 - - - +
18A TYR* 1.4 57.5 + - - +
21A GLU* 3.1 37.2 + - - +
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Residues in contact with TYR 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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15A PHE* 3.4 15.4 + + + +
17A ASP* 1.4 78.0 + - - +
19A PHE* 1.4 97.8 + + - +
21A GLU* 3.5 4.9 + - + +
22A GLU* 3.0 58.4 + - + +
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Residues in contact with PHE 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 PHE* 2.8 47.6 + + + +
16A MET* 5.2 0.4 - - - -
18A TYR* 1.4 99.0 - + - +
20A SER* 1.4 53.8 + - - +
22A GLU* 5.4 0.9 - - + -
23A PHE* 2.8 39.2 + - - +
56A ILE* 3.9 30.3 - - + +
60A ALA* 3.2 44.4 - - + +
61A THR* 5.3 5.4 - - + -
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Residues in contact with SER 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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16A MET* 2.9 47.8 + - - +
19A PHE* 1.4 73.9 - - - +
21A GLU* 1.4 56.0 + - - +
23A PHE* 4.5 4.0 - - - -
24A ARG* 2.8 32.2 + - - +
61A THR* 5.8 1.4 - - - +
63A TRP* 3.5 13.1 - - - -
72A TRP* 3.3 27.6 - - - -
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Residues in contact with GLU 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 ASP* 3.1 28.9 + - - +
18A TYR* 3.8 6.3 - - - +
19A PHE 3.4 0.4 - - - -
20A SER* 1.4 75.3 - - - +
22A GLU* 1.4 62.0 + - - +
25A ASN* 2.8 56.1 + - - +
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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 TYR* 3.0 46.9 + - + +
19A PHE* 4.7 0.9 - - + -
21A GLU* 1.4 78.3 - - + +
23A PHE* 1.4 63.2 + - - +
25A ASN* 4.7 4.0 - - - +
26A ASP* 3.3 34.2 + - - +
49A TYR* 4.0 5.5 + - - -
53A ARG* 3.5 27.6 + - - +
54A GLU* 5.1 4.3 - - + +
56A ILE* 4.2 14.8 - - + -
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Residues in contact with PHE 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 PHE 2.8 26.2 + - - +
20A SER 4.4 0.7 - - - +
22A GLU* 1.4 72.1 - - - +
24A ARG* 1.4 58.0 + - + +
27A PHE* 2.8 64.9 + + + +
46A TYR* 3.1 56.8 - + - +
49A TYR* 3.6 18.4 - + - +
56A ILE* 4.0 7.3 - - + +
61A THR* 4.6 1.8 - - + -
63A TRP* 3.9 23.1 - + - -
69A PHE* 3.2 42.6 - + - -
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Residues in contact with ARG 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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20A SER* 2.8 26.4 + - - +
21A GLU* 5.4 0.2 - - - -
23A PHE* 1.4 75.0 - - + +
25A ASN* 1.4 61.1 + - - +
27A PHE* 4.4 3.1 - - + -
28A LEU* 2.8 69.1 + - + +
63A TRP* 6.1 0.2 - - + -
69A PHE* 5.8 2.2 - - + -
72A TRP* 3.4 23.9 - - + -
73A LEU* 3.5 19.3 - - + -
76A GLU* 3.4 17.9 + - - -
78A LEU* 3.5 30.3 - - - +
95A ARG* 5.6 2.4 - - - +
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Residues in contact with ASN 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 GLU* 2.8 47.0 + - - +
22A GLU* 4.4 5.8 - - - +
24A ARG* 1.4 75.3 + - - +
26A ASP* 1.4 62.3 + - - +
28A LEU* 4.8 0.2 - - - +
29A GLU* 3.2 32.9 + - - +
32A ARG* 4.8 3.4 + - - +
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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* 3.3 27.7 + - - +
25A ASN* 1.4 77.8 - - - +
27A PHE* 1.4 54.2 + - - +
29A GLU* 3.0 24.5 - - - +
30A LEU* 2.8 37.1 + - - +
33A ARG* 5.4 2.3 + - - -
49A TYR* 3.7 7.8 - - + -
53A ARG* 3.4 33.7 + - - -
54A GLU* 3.5 32.2 - - - +
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Residues in contact with PHE 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 PHE* 2.8 55.5 + + + +
24A ARG* 4.4 2.2 - - - -
26A ASP* 1.4 67.9 - - - +
28A LEU* 1.4 56.2 + - - +
30A LEU* 3.7 3.1 - - - +
31A LEU* 2.8 51.5 + - + +
42A ASN* 3.3 35.7 - - - -
45A VAL* 3.5 22.3 - - + +
46A TYR* 3.4 27.1 - - - -
49A TYR* 3.5 15.1 - + + -
69A PHE* 3.8 24.0 - + - -
73A LEU* 4.6 10.3 - - + -
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Residues in contact with LEU 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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24A ARG* 2.8 43.9 + - + +
27A PHE* 1.4 72.2 - - + +
29A GLU* 1.4 55.7 + - - +
31A LEU* 3.7 20.7 - - + +
32A ARG* 3.0 60.7 + - - +
73A LEU* 3.6 31.6 - - + -
78A LEU* 3.4 42.0 - - + -
92A TYR* 4.0 8.3 - - + -
95A ARG* 4.9 1.6 - - - +
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Residues in contact with GLU 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 ASN* 3.2 17.6 + - - +
26A ASP* 3.0 35.7 - - - +
28A LEU* 1.4 75.0 - - - +
30A LEU* 1.4 54.4 + - - +
32A ARG* 3.2 10.9 + - - +
33A ARG* 2.9 59.8 + - - +
103A GLN* 3.8 16.0 - - - +
107A GLU* 3.9 14.2 - - - +
111A LYS* 5.0 6.4 + - - -
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Residues in contact with LEU 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 2.8 21.5 + - - +
27A PHE* 3.7 4.3 - - - +
29A GLU* 1.4 69.7 - - + +
31A LEU* 1.4 56.5 + - - +
33A ARG* 4.1 16.6 - - - +
34A ARG* 2.9 52.5 + - + +
35A PHE* 3.5 8.8 - - + -
45A VAL* 4.1 6.1 - - + +
48A GLU* 3.9 32.5 - - + +
49A TYR* 3.9 22.2 - - + +
52A HIS* 3.5 37.5 - - + +
54A GLU* 4.2 6.7 - - - +
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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 PHE* 2.8 28.5 + - + +
28A LEU* 3.7 18.4 - - + +
30A LEU* 1.4 70.2 - - - +
32A ARG* 1.4 57.8 + - - +
35A PHE* 3.3 22.1 - - + +
36A GLY 3.1 24.4 + - - +
38A LYS 5.7 1.1 - - - +
40A VAL* 4.4 13.2 - - + -
45A VAL* 4.2 28.5 - - + +
79A CYS* 3.9 9.0 - - - -
90A ILE* 4.1 11.0 - - + -
92A TYR* 3.3 47.1 - - + +
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Residues in contact with ARG 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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24A ARG 5.4 0.2 + - - -
25A ASN* 4.8 2.8 + - - +
28A LEU* 3.0 37.3 + - - +
29A GLU* 3.2 23.1 + - - +
31A LEU* 1.4 76.3 - - - +
33A ARG* 1.4 57.0 + - - +
36A GLY* 3.2 13.4 + - - +
92A TYR* 3.2 38.1 - - + +
95A ARG* 4.1 27.6 - - - +
99A THR* 4.3 12.1 - - - +
100A ILE* 3.6 14.2 - - + +
103A GLN* 3.3 34.5 + - - +
104A LEU* 3.0 21.0 - - - +
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Residues in contact with ARG 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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26A ASP* 5.4 2.2 + - - -
29A GLU* 2.9 49.9 + - - +
30A LEU* 4.2 13.5 - - - +
32A ARG* 1.4 70.7 - - - +
34A ARG* 1.3 95.7 - - + +
35A PHE 3.4 0.2 - - - -
52A HIS* 5.0 4.6 + - - -
103A GLN* 3.3 35.8 - - + +
104A LEU* 3.2 24.4 - - - +
107A GLU* 3.5 25.5 + - - +
108A LYS* 3.6 15.3 - - - +
111A LYS* 3.5 41.8 + - - +
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Residues in contact with ARG 34 (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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30A LEU* 2.9 31.5 + - + +
33A ARG* 1.3 110.1 - - + +
35A PHE* 1.4 63.9 + - + +
48A GLU* 3.8 26.6 + - - +
52A HIS* 3.6 35.6 + - - -
104A LEU* 5.3 0.2 - - - -
108A LYS* 3.5 25.0 - - - +
111A LYS 3.9 11.1 + - - -
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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