Contacts of the helix formed by residues 20 - 26 (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 LEU 20 (chain B).
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Specific contacts
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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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Residues in contact with TYR 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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18A SER 6.1 0.9 - - - -
22A SER* 4.6 18.2 - - - -
243A MET* 4.3 24.3 - - + +
247A LYS* 3.5 41.0 - - + +
17B TYR 5.2 0.4 - - - +
18B SER 4.4 10.7 + - - +
19B LEU 3.3 0.6 - - - +
20B LEU* 1.3 76.4 - - - +
22B SER* 1.3 56.2 + - - +
24B GLY* 3.0 6.0 + - - -
25B ASN* 2.3 73.4 + - - +
56B LEU* 5.0 2.5 - - - -
59B CYS* 4.1 15.5 - - - -
61B LEU* 3.5 22.9 - - + +
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Residues in contact with SER 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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21A TYR* 4.7 17.2 - - - -
18B SER 4.4 8.3 + - - -
19B LEU* 3.5 11.9 - - - -
21B TYR* 1.3 77.3 - - - +
23B ILE* 1.3 65.1 + - - +
24B GLY 3.2 0.2 - - - -
25B ASN* 3.5 17.5 + - - -
27B SER* 3.2 33.0 + - - -
28B VAL* 3.8 3.4 - - - +
246B ALA* 6.2 0.4 - - - -
250B CYS* 3.7 23.3 - - - -
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Residues in contact with ILE 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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6B VAL* 4.6 7.2 - - + -
8B VAL* 4.0 22.7 - - + -
19B LEU* 3.0 40.0 + - + +
20B LEU* 3.0 12.4 + - + +
22B SER* 1.3 78.5 - - - +
24B GLY* 1.3 62.1 + - - +
26B GLY* 3.5 9.4 + - - -
27B SER 4.5 0.2 + - - -
28B VAL* 4.2 17.8 + - + -
29B PHE* 3.8 26.6 - - + -
35B ILE* 3.1 31.7 - - + +
37B LEU* 4.8 10.3 - - + -
84B ILE* 4.1 14.8 - - + -
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Residues in contact with GLY 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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20B LEU 2.9 12.1 + - - -
21B TYR 3.0 7.0 + - - -
23B ILE* 1.3 79.8 - - - +
25B ASN* 1.4 56.4 + - - -
26B GLY 3.2 1.9 + - - -
35B ILE* 4.0 7.6 - - - +
37B LEU* 5.5 1.1 - - - +
56B LEU* 5.1 0.4 - - - -
61B LEU* 3.9 28.2 - - - +
63B LEU* 3.7 20.3 - - - +
64B LEU* 4.4 11.5 - - - +
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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
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21B TYR* 2.3 76.5 + - - +
22B SER* 3.5 14.2 + - - -
24B GLY* 1.4 67.7 - - - +
26B GLY* 1.4 56.9 + - - +
27B SER* 3.2 21.1 + - - +
31B LYS* 3.4 28.5 - - - +
61B LEU* 4.1 8.9 - - - +
63B LEU* 4.8 4.7 - - - +
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Residues in contact with GLY 26 (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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23B ILE 3.5 8.5 + - - -
24B GLY 3.2 5.1 - - - -
25B ASN* 1.4 78.5 - - - +
27B SER* 1.3 59.2 + - - +
28B VAL 3.2 6.4 + - - -
29B PHE* 5.1 1.1 - - - -
30B GLY* 3.6 38.3 + - - -
31B LYS* 3.7 13.4 + - - +
33B GLN 5.4 0.4 - - - -
35B ILE* 5.4 0.7 - - - -
63B LEU* 3.9 9.9 - - - -
254B ARG* 5.3 2.9 + - - -
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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