Contacts of the helix formed by residues 15 - 26 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.0 36.4 + - + +
12B THR 3.3 3.6 - - - -
13B LEU 3.2 0.4 - - - -
14B GLY* 1.3 87.7 + - - +
16B TRP* 1.3 62.5 + - - +
17B LYS 3.3 2.5 - - - -
18B ASP* 3.0 16.1 + - + +
19B VAL* 3.1 12.0 + - - +
96B TRP* 3.4 63.6 - + + +
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Residues in contact with TRP 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B THR 3.2 16.8 + - - -
13B LEU* 3.6 23.3 + - + +
14B GLY 3.6 1.8 - - - -
15B HIS* 1.3 76.1 - - - +
17B LYS* 1.4 67.7 + - + +
19B VAL* 3.1 18.0 + - + -
20B GLU* 2.9 49.8 + - + +
30B VAL* 3.7 30.7 - - + -
31B LYS 4.3 0.2 - - - -
32B LYS* 3.5 54.8 - - + +
35B TRP* 3.5 49.1 - + + -
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Residues in contact with LYS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B HIS 3.3 0.8 - - - -
16B TRP* 1.4 83.3 - - + +
18B ASP* 1.3 56.7 + - - +
20B GLU* 3.3 13.4 + - - +
21B ARG* 3.0 25.3 + - - +
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Residues in contact with ASP 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B HIS* 3.0 12.2 + - + +
17B LYS* 1.3 76.8 - - - +
19B VAL* 1.3 64.5 + - - +
21B ARG* 2.9 44.6 + - - +
22B ILE* 2.9 25.1 + - - +
94B PRO* 3.3 10.7 - - - +
96B TRP* 3.0 29.2 + - - +
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Residues in contact with VAL 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B THR* 3.6 35.2 - - + +
15B HIS 3.1 6.3 + - - +
16B TRP* 3.1 32.8 + - + +
18B ASP* 1.3 73.9 - - - +
20B GLU* 1.3 63.1 + - - +
22B ILE* 3.2 9.6 + - - +
23B ALA* 2.9 21.3 + - - +
30B VAL* 4.4 2.2 - - + -
35B TRP* 3.8 26.7 - - + -
85B THR* 4.0 7.7 - - + +
89B LEU* 4.9 4.0 - - + -
96B TRP* 3.8 20.8 - - + -
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Residues in contact with GLU 20 (chain B).
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* 2.9 31.6 + - - +
33A ARG* 4.8 5.4 + - - -
16B TRP* 2.9 50.0 + - + +
17B LYS* 3.5 15.0 - - - +
19B VAL* 1.3 76.0 - - - +
21B ARG* 1.3 55.7 + - - +
23B ALA* 3.2 7.0 + - - +
24B HIS* 2.8 53.3 + - + +
29B ASP* 4.6 1.3 - - - +
30B VAL* 4.4 4.7 - - + +
32B LYS 5.6 0.2 + - - -
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Residues in contact with ARG 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LYS 3.0 14.5 + - - +
18B ASP* 2.9 45.6 + - - +
20B GLU* 1.3 74.6 - - - +
22B ILE* 1.3 83.6 + - - +
24B HIS* 3.3 12.3 + - - +
25B ASN* 3.0 36.6 + - - +
92B ASP 5.6 3.8 + - - -
94B PRO* 3.9 11.9 - - - +
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Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ASP* 2.9 22.1 + - - +
19B VAL* 3.2 8.9 + - - +
21B ARG* 1.3 109.8 - - - +
23B ALA* 1.3 63.5 + - - +
25B ASN* 3.3 12.4 + - - +
26B GLN* 3.3 14.6 + - - +
85B THR* 4.1 11.2 - - + +
88B ALA* 3.8 27.1 - - + +
89B LEU* 3.4 42.2 - - + +
92B ASP 5.2 2.7 - - - +
94B PRO* 3.8 13.7 - - + -
96B TRP* 4.7 0.9 - - + -
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Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL 2.9 13.1 + - - +
20B GLU* 3.5 7.9 - - - +
22B ILE* 1.3 77.8 - - - +
24B HIS* 1.4 59.2 + - - +
26B GLN* 2.9 21.7 + - - +
27B SER 3.3 0.2 + - - -
28B VAL* 3.1 31.0 + - + +
29B ASP* 4.5 0.7 - - - -
30B VAL* 3.9 19.7 - - + +
85B THR* 3.3 28.9 - - + +
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Residues in contact with HIS 24 (chain B).
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* 5.2 0.2 - - - -
34A ARG* 6.2 0.6 + - - -
77A PRO* 3.1 20.9 - - + +
78A ASP* 3.5 37.5 + - + +
20B GLU* 2.8 44.9 + - + +
21B ARG* 3.3 9.4 + - - +
23B ALA* 1.4 72.3 - - - +
25B ASN* 1.3 58.2 + - - +
27B SER* 2.8 16.8 + - - -
28B VAL 3.3 14.6 + - - +
29B ASP* 3.1 32.5 - - - -
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Residues in contact with ASN 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PRO* 4.8 7.2 - - - +
21B ARG* 3.0 27.5 + - - +
22B ILE* 3.6 8.5 + - - +
23B ALA 3.2 0.4 - - - -
24B HIS* 1.3 75.2 - - - +
26B GLN* 1.3 74.5 + - - +
27B SER* 3.3 3.7 + - - -
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Residues in contact with GLN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE 3.3 11.8 + - - +
23B ALA* 2.9 10.5 + - - +
25B ASN* 1.3 99.3 + - - +
27B SER* 1.3 69.6 + - - +
28B VAL* 3.2 11.8 + - + +
84B VAL* 4.0 27.7 - - + +
85B THR* 5.3 0.4 - - - -
88B ALA* 3.7 28.4 - - + +
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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