Contacts of the helix formed by residues 31 - 41 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C LYS* 4.7 26.3 - - - +
16D TRP* 3.6 4.9 - - - +
20D GLU* 5.5 1.7 + - - -
29D ASP* 4.1 19.5 + - - +
30D VAL* 1.3 81.2 + - - +
32D LYS* 1.3 66.4 + - - +
33D ARG* 3.4 3.8 + - + +
34D ARG* 3.5 17.1 + - + +
35D TRP* 3.0 22.9 + - - +
82D TYR* 3.0 16.1 + - - +
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Residues in contact with LYS 32 (chain D).
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 3.6 26.2 - - - +
14A GLY* 4.2 12.1 - - - -
16A TRP* 5.2 5.4 - - - +
32A LYS* 5.1 11.6 - - - +
17C LYS* 5.4 5.3 - - - +
13D LEU* 4.3 6.1 - - + +
16D TRP* 3.4 54.6 - - + +
20D GLU* 5.4 1.0 + - - -
31D LYS* 1.3 74.5 - - - +
33D ARG* 1.3 93.6 + - - +
35D TRP* 3.3 2.3 + - - +
36D VAL* 3.1 16.1 + - - +
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Residues in contact with ARG 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 6.2 0.2 - - - +
14A GLY* 2.5 28.9 + - - -
15A HIS* 3.2 42.0 + - + +
13D LEU* 3.4 13.1 - - - +
31D LYS* 3.4 2.4 - - + +
32D LYS* 1.3 111.9 + - + +
34D ARG* 1.3 58.7 + - - +
36D VAL* 2.8 34.0 + - - +
37D THR* 2.9 32.3 + - - -
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Residues in contact with ARG 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LYS* 3.5 15.1 + - + +
32D LYS 3.2 0.2 - - - -
33D ARG* 1.3 76.7 - - - +
35D TRP* 1.3 65.6 + - - +
37D THR* 4.3 7.6 - - - -
38D PHE* 2.9 65.1 + - + -
78D ASP* 6.3 1.4 - - - +
82D TYR* 3.4 27.9 + - + +
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Residues in contact with TRP 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 3.8 13.8 - - + +
12D THR* 2.9 39.1 + - + -
13D LEU* 4.8 2.7 - - + -
16D TRP* 3.6 27.6 - + + -
19D VAL* 3.8 13.5 - - + -
30D VAL* 4.2 6.1 - - + -
31D LYS 3.0 19.1 + - - +
32D LYS 3.4 5.4 - - - +
34D ARG* 1.3 77.3 - - - +
36D VAL* 1.3 65.8 + - + +
38D PHE* 4.1 1.7 - - - +
39D CYS* 3.0 26.5 + - - +
43D TRP* 5.8 0.2 - - - -
82D TYR* 3.5 31.5 - + + -
85D THR* 3.7 31.2 - - - -
86D TRP* 3.3 58.8 + + - -
89D LEU* 4.3 4.5 - - + -
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Residues in contact with VAL 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A THR* 5.9 2.5 - - + +
6A THR* 6.1 1.1 - - + -
11A LEU* 6.4 2.0 - - + -
15A HIS* 6.1 0.7 - - + -
9D LEU* 4.2 21.8 - - + -
13D LEU* 4.0 23.3 - - + -
32D LYS 3.1 2.9 + - - +
33D ARG* 2.8 48.7 - - - +
35D TRP* 1.3 76.4 - - + +
37D THR* 1.3 63.4 + - - +
39D CYS* 3.8 0.2 - - - +
40D SER* 2.8 39.9 + - - +
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Residues in contact with THR 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ARG* 2.9 17.8 + - - +
34D ARG* 3.2 11.1 + - - -
36D VAL* 1.3 78.9 - - - +
38D PHE* 1.3 69.5 + - + +
40D SER* 4.2 3.8 - - - -
41D ALA* 2.9 37.5 + - + -
42D GLU* 3.1 9.2 + - + +
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Residues in contact with PHE 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ARG* 2.9 50.8 + - + +
35D TRP 4.2 2.2 - - - +
37D THR* 1.3 85.2 - - + +
39D CYS* 1.3 60.3 + - - +
42D GLU* 3.5 17.7 + - + -
43D TRP* 2.9 54.4 + - + -
78D ASP* 3.8 22.4 - - + -
79D GLN* 3.6 36.6 - - + -
82D TYR* 3.6 34.1 - + + -
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Residues in contact with CYS 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 3.9 15.0 - - + -
35D TRP 3.0 19.3 + - - +
36D VAL 3.8 2.9 - - - +
38D PHE* 1.3 76.1 - - - +
40D SER* 1.3 58.7 + - - +
43D TRP* 4.1 5.7 - - + -
44D PRO* 3.3 13.3 - - - +
50D TRP* 3.0 29.4 + - - +
52D ARG 3.6 9.2 - - - +
54D GLY* 3.4 38.4 - - - -
86D TRP* 3.8 24.5 - - + +
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Residues in contact with SER 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLN* 4.0 20.6 + - - +
4A THR* 3.5 24.7 - - - -
9D LEU* 4.5 6.1 - - - -
36D VAL* 2.8 30.8 + - - +
37D THR* 4.1 2.3 + - - -
39D CYS* 1.3 78.8 - - - +
41D ALA* 1.3 62.5 + - - +
44D PRO* 3.7 4.1 - - - +
52D ARG* 3.3 31.1 - - - +
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Residues in contact with ALA 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLN* 6.1 1.6 - - - +
37D THR* 2.9 23.7 + - + +
40D SER* 1.3 84.1 + - - +
42D GLU* 1.3 61.5 + - - +
43D TRP 3.8 0.2 - - - -
44D PRO* 3.8 4.9 - - - +
45D THR* 3.4 20.3 - - - +
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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