Contacts of the helix formed by residues 7 - 15 (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 THR 7 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL 3.3 1.1 + - - +
6A THR* 1.3 77.3 - - - +
8A PRO* 1.3 75.7 - - - +
9A LEU* 3.8 0.9 + - - +
10A SER* 3.0 25.5 + - - -
11A LEU* 2.9 21.0 + - - +
53A ASP* 3.6 33.7 - - + +
3D GLN 3.5 16.4 - - - +
4D THR 4.8 0.9 - - - -
5D VAL 3.8 22.7 - - - +
6D THR* 5.2 0.2 - - - -
10D SER* 4.2 13.5 - - - +
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Residues in contact with PRO 8 (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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6A THR 4.1 1.3 - - - +
7A THR* 1.3 82.7 - - - +
9A LEU* 1.4 63.6 + - - +
11A LEU* 3.2 4.9 + - + +
12A THR* 2.9 28.3 + - - +
53A ASP 3.4 13.9 - - - +
54A GLY* 3.5 23.6 - - - +
55A THR* 3.7 9.0 - - - +
56A PHE* 3.7 34.0 - - + -
86A TRP* 4.5 2.0 - - + -
2D GLY* 3.8 17.0 - - - -
3D GLN 3.5 21.3 - - - +
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Residues in contact with LEU 9 (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 THR* 4.3 1.8 - - - +
8A PRO* 1.4 72.4 - - - +
10A SER* 1.3 64.6 + - - +
12A THR* 2.7 20.8 + - - +
13A LEU* 3.0 19.7 + - + +
35A TRP* 3.8 31.0 - - + +
36A VAL* 4.4 26.7 - - + -
39A CYS* 4.1 20.6 - - + -
40A SER* 4.6 5.4 - - - -
52A ARG 4.1 11.4 - - - +
53A ASP* 2.8 44.2 + - - +
86A TRP* 4.3 4.6 - - + -
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Residues in contact with SER 10 (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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6A THR* 4.8 1.3 - - - -
7A THR* 3.0 23.8 + - - -
9A LEU* 1.3 78.7 - - - +
11A LEU* 1.3 57.8 + - - +
13A LEU* 3.3 10.1 + - - +
14A GLY 2.9 23.9 + - - -
53A ASP* 5.6 0.7 + - - -
10D SER* 2.7 41.5 + - - -
13D LEU* 3.7 19.9 - - - +
14D GLY* 3.9 8.1 + - - -
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Residues in contact with LEU 11 (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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4A THR* 5.3 4.5 - - + -
6A THR* 3.0 39.0 - - + +
7A THR 2.9 9.7 + - - +
8A PRO* 3.4 6.7 - - + +
10A SER* 1.3 77.5 - - - +
12A THR* 1.4 62.7 + - - +
14A GLY* 3.1 6.3 + - - +
15A HIS* 3.1 39.2 + - + +
56A PHE* 4.0 24.0 - - + -
96A TRP* 3.8 25.5 - - + +
97A VAL* 4.9 4.7 - - + -
13D LEU* 5.2 3.8 - - + -
33D ARG* 6.2 0.2 - - - +
36D VAL* 6.4 2.0 - - + -
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Residues in contact with THR 12 (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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8A PRO 2.9 18.0 + - - +
9A LEU* 2.7 20.3 + - - +
11A LEU* 1.4 75.3 - - - +
13A LEU* 1.3 61.4 + - - +
15A HIS 3.2 4.2 + - - -
16A TRP* 3.1 25.7 + - - -
19A VAL* 3.7 11.0 - - - +
35A TRP* 2.9 33.1 + - + -
56A PHE* 4.0 13.9 - - + -
86A TRP* 4.1 5.4 - - + -
89A LEU* 3.9 27.1 - - + -
96A TRP* 4.0 10.5 - - + -
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Residues in contact with LEU 13 (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* 3.0 28.8 + - + +
10A SER* 3.7 10.3 - - - +
11A LEU 3.2 0.2 - - - -
12A THR* 1.3 77.5 - - - +
14A GLY* 1.3 62.1 - - - +
15A HIS 3.3 0.5 + - - -
16A TRP* 3.6 20.8 + - + +
32A LYS* 3.7 36.5 + - + +
35A TRP* 4.5 6.5 - - + -
36A VAL* 3.9 26.0 - - + -
13D LEU* 4.2 12.1 - - - +
14D GLY* 4.0 28.3 - - - +
32D LYS* 3.6 18.8 - - + +
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Residues in contact with GLY 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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10A SER 2.9 14.9 + - - -
11A LEU* 3.1 5.1 + - - -
13A LEU* 1.3 76.0 - - - +
15A HIS* 1.3 58.7 + - - +
16A TRP 3.6 0.9 - - - -
13D LEU* 4.3 6.0 - - - +
32D LYS* 4.2 11.4 - - - -
33D ARG* 2.5 54.8 + - - -
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Residues in contact with HIS 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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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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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