Contacts of the helix formed by residues 13 - 20 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLY 2.6 19.1 + - - -
11B ALA 3.4 0.2 - - - -
12B ALA* 1.3 77.0 - - - +
14B GLN* 1.3 64.4 + - - -
15B ILE 3.8 1.1 - - - -
16B ALA* 3.9 3.4 + - - +
17B TYR* 3.4 21.3 + - - +
335B NAD 2.8 33.4 + - - -
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Residues in contact with GLN 14 (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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13B GLY* 1.3 69.3 - - - -
15B ILE* 1.3 69.7 + - - +
16B ALA 3.2 1.1 - - - -
17B TYR* 3.4 12.7 + - - +
18B SER* 3.6 6.1 + - - -
237B ARG* 4.6 3.3 + - - +
239B LEU* 3.5 26.4 - - - +
240B SER* 2.3 42.5 + - - +
242B ALA* 3.5 12.8 - - + +
335B NAD 2.8 33.8 + - - +
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Residues in contact with ILE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLN* 1.3 74.5 - - - +
16B ALA* 1.4 63.5 + - - +
18B SER* 2.9 15.2 + - - -
19B LEU* 3.1 18.2 + - + +
86B VAL* 4.5 8.3 - - + -
128B VAL* 4.5 7.0 - - + -
240B SER* 5.2 2.2 - - - -
241B SER 5.6 1.3 - - - +
242B ALA* 4.0 15.5 - - + +
245B ALA* 3.7 22.0 - - + -
246B ALA* 4.1 17.3 - - + +
249B ILE* 3.9 23.1 - - + -
335B NAD 3.1 59.9 + - + +
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Residues in contact with ALA 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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8B VAL* 4.1 15.0 - - + -
9B THR 4.9 0.7 - - - +
10B GLY 4.1 7.0 - - - +
11B ALA* 3.6 38.4 - - + +
13B GLY 3.9 3.2 + - - +
14B GLN 3.2 0.8 - - - -
15B ILE* 1.4 77.7 - - - +
17B TYR* 1.3 58.1 - - - +
19B LEU* 4.0 10.5 - - - -
20B LEU* 2.9 38.1 + - + +
86B VAL* 5.1 4.8 - - + +
335B NAD 4.6 1.0 + - - -
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Residues in contact with TYR 17 (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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14A GLN* 4.3 8.1 - - + -
18A SER* 3.9 22.7 + - - -
237A ARG* 3.6 26.3 + - - -
242A ALA* 3.0 15.2 - - + +
243A MET* 2.8 61.9 + - + +
11B ALA 5.0 2.2 + - - +
12B ALA 5.6 0.2 - - - +
13B GLY 3.4 15.5 + - - +
14B GLN* 3.4 8.7 + - - +
15B ILE 3.2 1.0 + - - -
16B ALA* 1.3 78.4 - - - +
18B SER* 1.3 60.1 + - - +
20B LEU* 4.6 1.4 + - - -
21B TYR* 4.9 1.9 + - - +
52B VAL* 4.0 19.1 - - + -
55B GLU* 2.7 28.2 + - - -
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Residues in contact with SER 18 (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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17A TYR* 4.0 15.8 + - - -
18A SER* 5.4 4.9 + - - -
14B GLN 3.6 2.7 + - - -
15B ILE 2.9 9.1 + - - -
17B TYR* 1.3 82.0 - - - +
19B LEU* 1.3 61.7 + - - +
20B LEU 3.7 0.2 - - - -
21B TYR* 4.4 9.0 + - - +
22B SER* 4.4 11.3 + - - -
242B ALA* 3.7 34.8 - - - +
243B MET* 4.2 4.9 + - - -
246B ALA* 3.8 7.7 - - - +
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Residues in contact with LEU 19 (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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8B VAL* 4.3 24.5 - - + -
15B ILE* 3.1 15.6 + - + +
16B ALA* 3.2 5.8 + - - +
18B SER* 1.3 77.2 - - - +
20B LEU* 1.3 67.3 + - - +
21B TYR 3.3 1.7 + - - -
22B SER* 3.3 5.1 + - - -
23B ILE* 3.0 43.0 + - + +
84B ILE* 4.6 9.6 - - + -
86B VAL* 4.6 9.2 - - + -
246B ALA* 3.9 12.6 - - + +
249B ILE* 3.7 37.7 - - + -
250B CYS* 4.1 14.8 - - - -
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Residues in contact with LEU 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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243A MET* 4.1 9.4 - - + -
8B VAL* 3.9 21.1 - - + -
11B ALA* 4.8 10.1 - - + +
16B ALA* 2.9 23.8 + - + +
18B SER 3.7 0.2 - - - -
19B LEU* 1.3 77.1 - - - +
21B TYR* 1.3 62.9 - - - +
23B ILE* 3.0 7.3 + - + +
24B GLY* 2.9 19.1 + - - -
37B LEU* 3.7 34.3 - - + +
39B LEU* 3.8 21.8 - - + -
52B VAL* 4.1 12.1 - - + -
56B LEU* 3.4 35.3 - - + +
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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