Contacts of the helix formed by residues 31 - 41 (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 LYS 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A TRP* 3.9 1.6 - - - -
30A VAL* 1.3 73.0 - - - +
32A LYS* 1.3 65.1 + - - +
33A ARG* 3.8 34.5 - - - +
34A ARG* 3.2 17.8 + - + +
35A TRP* 2.9 23.2 + - - +
82A TYR* 2.9 12.9 + - - +
20B GLU* 2.9 31.7 + - - -
24B HIS* 5.2 0.2 - - - -
29B ASP* 2.9 29.4 + - + +
30B VAL 2.9 29.0 + - - -
31B LYS* 3.8 26.5 - - + +
32B LYS 5.4 0.2 - - - +
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Residues in contact with LYS 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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13A LEU* 3.7 30.0 + - + +
16A TRP* 3.5 61.2 - - + +
30A VAL 4.0 0.2 + - - -
31A LYS* 1.3 70.1 - - - +
33A ARG* 1.3 65.4 + - - +
35A TRP* 3.2 3.3 + - - +
36A VAL* 3.0 25.3 + - + +
31B LYS* 5.0 0.6 - - - +
16D TRP* 6.3 0.6 - - - -
17D LYS* 5.7 6.9 - - - +
32D LYS* 5.1 10.3 - - - +
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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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31A LYS* 3.8 42.1 - - - +
32A LYS* 1.3 81.4 - - - +
34A ARG* 1.4 74.3 + - + +
36A VAL* 3.5 6.9 + - - +
37A THR* 3.0 32.0 + - - +
20B GLU* 4.8 4.8 + - - -
31B LYS* 6.1 0.2 - - - +
33C ARG* 3.4 61.1 - - - +
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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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31A LYS* 3.2 21.8 + - + +
33A ARG* 1.4 89.4 - - + +
35A TRP* 1.3 59.2 + - - +
36A VAL 3.2 0.4 - - - -
37A THR* 3.9 27.4 + - - +
38A PHE* 2.8 71.6 + - + -
78A ASP* 4.5 6.3 + - - -
82A TYR* 3.5 29.2 - - + +
24B HIS* 6.2 0.6 + - - -
29B ASP* 4.4 3.5 + - - +
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Residues in contact with TRP 35 (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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9A LEU* 3.8 15.9 - - + +
12A THR* 2.9 34.4 + - + -
13A LEU* 4.5 7.0 - - + -
16A TRP* 3.6 29.6 - + + -
19A VAL* 3.7 18.8 - - + -
30A VAL* 4.5 2.9 - - + -
31A LYS 2.9 13.6 + - - +
32A LYS 3.3 8.5 - - - +
34A ARG* 1.3 76.0 - - - +
36A VAL* 1.3 61.4 + - - +
38A PHE* 4.1 1.7 - - - +
39A CYS* 3.0 26.3 + - - +
43A TRP* 5.8 0.3 - - - -
82A TYR* 3.6 32.4 - + + -
85A THR* 3.6 28.3 - - + -
86A TRP* 3.2 62.1 + + - +
89A LEU* 4.4 3.8 - - + -
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Residues in contact with VAL 36 (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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9A LEU* 4.4 19.5 - - + -
13A LEU* 3.9 35.2 - - + -
32A LYS* 3.0 16.0 + - + +
33A ARG* 3.7 9.2 - - - +
35A TRP* 1.3 73.5 - - + +
37A THR* 1.3 67.0 + - - +
39A CYS* 3.3 0.7 + - - +
40A SER* 2.8 40.5 + - - +
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Residues in contact with THR 37 (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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33A ARG* 3.0 18.4 + - - +
34A ARG* 3.3 28.0 + - - +
36A VAL* 1.3 79.0 - - - +
38A PHE* 1.3 61.8 + - + +
40A SER* 4.2 4.0 - - - -
41A ALA* 2.9 37.3 + - + +
42A GLU* 3.1 22.3 + - + +
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Residues in contact with PHE 38 (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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34A ARG* 2.8 60.0 + - + +
35A TRP* 4.2 2.5 - - - +
37A THR* 1.3 75.7 - - + +
39A CYS* 1.3 62.3 + - - +
42A GLU* 3.5 21.9 + - + -
43A TRP* 2.9 53.3 + - + +
78A ASP* 3.7 18.8 - - + -
79A GLN* 3.7 36.3 - - + -
82A TYR* 3.5 45.1 - + + -
29B ASP* 5.6 0.4 - - - -
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Residues in contact with CYS 39 (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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9A LEU* 4.1 16.8 - - + -
35A TRP 3.0 19.3 + - - +
36A VAL 3.7 3.1 - - - +
38A PHE* 1.3 77.4 - - - +
40A SER* 1.4 56.9 + - - +
43A TRP* 4.1 6.1 - - + -
44A PRO* 3.3 14.2 - - - +
50A TRP* 3.2 32.4 + - - +
52A ARG 3.4 11.3 - - - +
53A ASP 4.1 1.8 - - - -
54A GLY* 3.5 33.4 - - - -
86A TRP* 3.8 20.9 - - + +
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Residues in contact with SER 40 (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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9A LEU* 4.6 9.2 - - - -
36A VAL* 2.8 32.0 + - - +
37A THR* 4.2 2.3 - - - -
39A CYS* 1.4 77.5 - - - +
41A ALA* 1.3 62.7 + - - +
44A PRO* 3.6 13.5 - - - +
52A ARG* 3.3 43.7 + - - +
53A ASP* 5.4 1.1 - - - -
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Residues in contact with ALA 41 (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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37A THR* 2.9 25.9 + - + +
40A SER* 1.3 83.0 - - - +
42A GLU* 1.3 71.5 + - - +
44A PRO* 3.8 4.7 - - - +
45A THR* 3.3 21.3 - - - +
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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