Contacts of the helix formed by residues 13 - 20 (chain A) in PDB entry 4MDH
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 GLY 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLY 3.4 8.3 + - - -
11A ALA 3.4 0.7 - - - +
12A ALA* 1.3 81.4 - - - +
14A GLN* 1.3 60.8 + - - -
15A ILE 3.6 2.0 - - - -
16A ALA* 3.7 2.9 - - - +
17A TYR* 3.0 31.3 + - - +
335A NAD 3.5 26.9 + - - -
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Residues in contact with GLN 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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13A GLY* 1.3 69.3 - - - -
15A ILE* 1.3 64.8 + - - +
17A TYR* 3.5 11.2 + - - +
18A SER* 3.5 14.2 + - - -
237A ARG* 2.7 27.6 + - - +
239A LEU* 3.9 16.1 - - - +
240A SER 2.8 27.9 + - - +
242A ALA* 3.1 20.8 - - + +
335A NAD 3.4 35.3 + - - +
17B TYR* 4.1 6.8 + - + -
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Residues in contact with ILE 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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14A GLN* 1.3 73.3 - - - +
16A ALA* 1.3 53.7 + - - +
18A SER* 3.2 4.2 + - - -
19A LEU* 2.9 31.1 + - + +
86A VAL* 4.2 13.2 - - + -
128A VAL* 4.5 4.7 - - + -
241A SER 3.4 19.1 - - - +
242A ALA* 3.8 10.1 - - - +
245A ALA* 3.9 7.4 - - + -
246A ALA* 3.9 14.8 - - + +
249A ILE* 3.8 26.9 - - + -
335A NAD 3.0 68.6 + - + +
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Residues in contact with ALA 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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8A VAL* 4.5 10.3 - - + -
9A THR 4.8 0.4 - - - +
10A GLY 3.1 27.7 + - - +
11A ALA* 3.5 25.8 - - + +
13A GLY 3.7 4.7 - - - +
15A ILE* 1.3 78.2 - - - +
17A TYR* 1.3 58.2 + - - +
19A LEU* 3.7 10.8 - - - -
20A LEU* 3.1 36.9 + - + +
86A VAL* 4.9 3.5 - - + +
335A NAD 4.8 0.4 + - - -
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Residues in contact with TYR 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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11A ALA 5.7 1.1 - - - -
13A GLY 3.0 19.5 + - - +
14A GLN* 3.9 6.5 - - - +
15A ILE 3.1 0.4 - - - -
16A ALA* 1.3 78.7 - - - +
18A SER* 1.4 60.1 + - - +
20A LEU* 4.4 3.4 + - - -
21A TYR* 4.9 2.6 + - - +
52A VAL* 4.3 16.6 - - + -
55A GLU* 2.6 30.3 + - - -
18B SER* 4.0 12.0 + - - -
237B ARG* 3.3 44.7 + - - +
242B ALA* 3.0 19.5 + - + -
243B MET* 2.6 61.8 + - + +
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Residues in contact with SER 18 (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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14A GLN 3.5 10.0 + - - -
15A ILE 3.2 5.2 + - - -
17A TYR* 1.4 79.4 - - - +
19A LEU* 1.3 62.3 + - - +
21A TYR* 4.7 4.5 + - - +
22A SER* 4.1 10.2 + - - -
242A ALA 4.1 7.9 - - - -
243A MET* 4.1 6.7 + - - +
246A ALA* 3.7 21.4 - - - +
17B TYR* 3.9 25.6 + - - -
18B SER* 5.4 5.0 + - - -
21B TYR* 6.1 0.9 - - - -
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Residues in contact with LEU 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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8A VAL* 4.3 22.7 - - + -
15A ILE* 2.9 17.5 + - + +
16A ALA* 4.0 4.7 - - - +
17A TYR 3.4 0.4 - - - -
18A SER* 1.3 81.1 - - - +
20A LEU* 1.3 60.1 + - + +
21A TYR 3.3 0.2 - - - -
22A SER* 2.9 22.2 + - - -
23A ILE* 3.2 32.7 + - + -
84A ILE* 4.6 5.8 - - + -
86A VAL* 5.0 2.7 - - + -
246A ALA* 3.5 29.4 - - + +
249A ILE* 3.9 33.4 - - + -
250A CYS* 3.6 19.7 - - - -
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Residues in contact with LEU 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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8A VAL* 4.2 19.7 - - + -
11A ALA 4.5 9.9 - - - +
16A ALA* 3.1 26.9 + - + +
17A TYR* 4.4 1.0 + - - -
18A SER 3.7 0.4 - - - -
19A LEU* 1.3 74.3 - - + +
21A TYR* 1.3 61.9 + - - +
23A ILE* 3.3 8.4 + - + +
24A GLY* 3.1 20.6 + - - -
37A LEU* 3.5 27.7 - - + +
39A LEU* 3.8 25.8 - - + -
52A VAL* 3.9 27.6 - - + -
56A LEU* 4.1 25.0 - - + +
64A LEU* 5.8 0.3 - - - +
243B MET* 4.7 6.1 - - + -
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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