Contacts of the helix formed by residues 15 - 26 (chain A) in PDB entry 1MN8
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 HIS 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.1 35.8 + - + +
12A THR 3.2 3.1 - - - -
13A LEU 3.1 0.4 - - - -
14A GLY* 1.3 75.1 - - - +
16A TRP* 1.3 65.4 + - - +
17A LYS 3.3 2.5 - - - -
18A ASP* 3.0 16.5 + - + +
19A VAL* 3.2 10.7 + - - +
96A TRP* 3.5 61.2 - + + +
33D ARG* 3.2 37.5 + - - +
36D VAL* 6.1 0.9 - - + -
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Residues in contact with TRP 16 (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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12A THR 3.1 16.9 + - - -
13A LEU* 3.6 21.3 + - + +
14A GLY 3.6 0.8 - - - -
15A HIS* 1.3 76.6 - - - +
17A LYS* 1.3 66.1 + - - +
19A VAL* 3.0 20.5 + - + +
20A GLU* 2.9 47.8 + - + +
30A VAL* 3.7 33.0 - - + -
32A LYS* 3.5 69.8 - - + +
35A TRP* 3.6 37.7 - + + -
32D LYS* 5.2 5.6 - - - +
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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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15A HIS 3.3 0.8 + - - -
16A TRP* 1.3 81.6 - - - +
18A ASP* 1.3 57.7 + - - +
20A GLU* 2.5 46.8 + - - +
21A ARG* 3.0 28.4 + - + +
24A HIS* 3.7 12.4 + - - -
34B ARG* 4.6 2.2 - - - +
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Residues in contact with ASP 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A HIS* 3.0 13.2 + - + +
17A LYS* 1.3 76.4 - - - +
19A VAL* 1.4 65.2 + - - +
21A ARG* 2.8 46.9 + - - +
22A ILE* 3.0 23.8 + - - +
94A PRO* 3.3 10.0 - - - +
96A TRP* 2.9 30.3 + - + +
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Residues in contact with VAL 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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12A THR* 3.7 34.3 - - + +
15A HIS 3.2 6.3 + - - +
16A TRP* 3.0 32.4 + - + +
18A ASP* 1.4 75.8 - - - +
20A GLU* 1.4 61.9 + - - +
22A ILE* 3.2 10.1 + - - +
23A ALA* 2.9 21.1 + - - +
30A VAL* 4.4 2.2 - - + -
35A TRP* 3.7 24.9 - - + -
85A THR* 3.9 8.8 - - + +
89A LEU* 4.6 5.4 - - + -
96A TRP* 3.9 20.4 - - + -
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Residues in contact with GLU 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 TRP* 2.9 48.0 + - + +
17A LYS* 2.5 31.5 + - - +
18A ASP 3.2 0.2 - - - -
19A VAL* 1.4 77.5 - - - +
21A ARG* 1.3 54.8 + - - +
23A ALA* 3.2 6.9 + - - +
24A HIS* 2.8 39.1 + - + +
29A ASP* 4.9 1.3 - - - +
30A VAL* 4.4 5.6 - - + +
31B LYS* 2.9 26.8 + - - +
33B ARG* 4.4 4.6 + - - -
34B ARG* 2.8 33.1 + - - +
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Residues in contact with ARG 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* 3.0 24.8 + - + +
18A ASP* 2.8 45.8 + - - +
20A GLU* 1.3 74.3 - - - +
22A ILE* 1.3 87.7 + - - +
24A HIS* 3.3 9.0 + - - +
25A ASN* 3.0 33.7 + - - +
92A ASP* 5.4 11.1 + - - -
94A PRO* 3.7 16.2 - - - +
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Residues in contact with ILE 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 ASP* 3.0 18.4 + - - +
19A VAL* 3.5 11.0 - - - +
21A ARG* 1.3 105.6 - - - +
23A ALA* 1.3 67.7 + - - +
25A ASN* 3.3 12.4 + - - +
26A GLN* 3.3 14.0 + - - +
85A THR* 4.0 11.2 - - + +
88A ALA* 3.8 27.6 - - + -
89A LEU* 3.8 25.1 - - + +
92A ASP 5.3 3.1 - - - +
94A PRO* 4.0 25.4 - - + -
96A TRP* 4.7 2.9 - - + -
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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 VAL 2.9 13.1 + - - +
20A GLU* 3.2 8.5 + - - +
22A ILE* 1.3 77.9 - - - +
24A HIS* 1.4 57.3 + - - +
26A GLN* 2.8 22.0 + - - +
27A SER 3.2 0.2 + - - -
28A VAL* 3.1 31.8 + - + +
29A ASP* 4.5 2.0 - - - -
30A VAL* 3.9 17.9 - - + -
85A THR* 3.3 29.8 - - + +
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Residues in contact with HIS 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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17A LYS* 3.7 18.8 + - - -
20A GLU* 2.8 34.4 + - + +
21A ARG* 3.3 8.9 + - - +
23A ALA* 1.4 72.6 - - + +
25A ASN* 1.3 59.0 + - - +
27A SER* 2.8 16.6 + - - -
28A VAL 3.3 15.2 + - - +
29A ASP* 3.1 29.3 - - - -
34B ARG* 3.7 15.8 + - - -
77B PRO* 3.1 20.8 - - + +
78B ASP* 3.6 34.6 + - + +
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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 ARG* 3.0 29.4 + - - +
22A ILE* 3.7 8.3 + - - +
23A ALA 3.2 0.2 - - - -
24A HIS* 1.3 75.4 - - - +
26A GLN* 1.3 75.1 + - - +
27A SER* 3.3 4.2 + - - -
92A ASP* 5.2 7.9 + - - -
77B PRO* 4.8 6.3 - - - +
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Residues in contact with GLN 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 ILE 3.3 11.8 + - - +
23A ALA* 2.8 11.5 + - - +
25A ASN* 1.3 99.0 + - - +
27A SER* 1.3 69.5 + - - +
28A VAL* 3.2 11.5 + - + +
84A VAL* 3.9 27.8 - - + +
85A THR* 5.4 0.2 - - - -
88A ALA* 3.7 30.3 - - + +
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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
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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