Contacts of the helix formed by residues 45 - 60 (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 MET 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B ALA* 4.2 7.9 - - + +
41B ASP* 3.1 24.2 - - + +
42B ILE* 2.8 36.5 + - + +
43B THR 2.7 2.8 + - - -
44B PRO* 1.3 92.5 - - + +
46B MET* 1.3 57.8 + - - +
47B GLY 3.3 3.4 - - - -
48B VAL* 3.5 19.2 + - - +
49B LEU* 3.0 27.5 + - - +
335B NAD 3.4 14.6 - - - +
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Residues in contact with MET 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ASP 5.3 1.1 - - - +
42B ILE 4.3 4.7 - - - +
43B THR* 2.8 17.7 + - + +
44B PRO 3.5 0.4 - - - -
45B MET* 1.3 75.6 - - - +
47B GLY* 1.4 55.8 + - - +
49B LEU* 3.7 10.9 - - + +
50B ASP* 2.3 56.8 + - - +
69B ALA* 4.6 14.1 - - + +
70B THR* 4.1 12.8 - - - +
71B ASP* 3.9 39.7 - - + -
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Residues in contact with GLY 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ALA* 3.6 19.4 - - - +
44B PRO 5.1 1.8 + - - -
45B MET 3.3 0.8 - - - -
46B MET* 1.4 71.2 - - - +
48B VAL* 1.3 65.7 + - - +
49B LEU 3.1 0.9 - - - -
50B ASP* 3.0 17.7 + - - +
51B GLY 3.1 9.2 + - - -
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Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ALA 3.5 18.3 + - - +
237A ARG* 3.6 22.7 - - + +
238A LYS* 5.5 3.4 - - + -
12B ALA* 3.7 27.4 - - + +
44B PRO 5.7 0.7 - - - +
45B MET* 3.5 22.4 + - - +
47B GLY* 1.3 75.5 - - - +
49B LEU* 1.3 58.5 + - - +
51B GLY 3.3 0.9 + - - -
52B VAL* 3.0 35.6 + - + +
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Residues in contact with LEU 49 (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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11B ALA* 3.5 43.1 - - + +
12B ALA* 3.7 9.0 - - + +
39B LEU* 3.8 29.7 - - + +
41B ASP* 4.3 10.8 - - + +
45B MET 3.0 17.3 + - - +
46B MET* 3.9 15.5 - - + +
47B GLY 3.1 0.4 - - - -
48B VAL* 1.3 75.2 - - - +
50B ASP* 1.3 60.1 + - - +
52B VAL* 3.3 5.8 + - + +
53B LEU* 2.8 26.0 + - - +
69B ALA* 3.3 28.5 - - + -
70B THR 3.9 10.8 - - - +
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Residues in contact with ASP 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ALA* 5.3 0.4 - - + -
46B MET* 2.3 44.6 + - - +
47B GLY* 3.0 9.3 + - - +
49B LEU* 1.3 72.4 - - - +
51B GLY* 1.3 57.2 + - - +
53B LEU* 2.8 13.0 + - + +
54B MET* 2.7 48.9 + - + +
69B ALA* 4.2 9.2 - - - +
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Residues in contact with GLY 51 (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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233A VAL* 4.2 4.3 - - - +
236A ALA* 3.2 27.0 - - - +
237A ARG* 3.8 13.0 - - - -
47B GLY 3.1 10.5 + - - -
48B VAL 3.3 3.6 + - - -
49B LEU 3.2 0.2 - - - -
50B ASP* 1.3 76.6 - - - +
52B VAL* 1.3 55.1 + - - +
54B MET* 3.1 25.3 + - - +
55B GLU* 3.1 17.3 + - - +
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ARG* 3.4 20.9 - - - +
243A MET* 4.4 11.8 - - + +
11B ALA 4.3 14.6 - - - +
12B ALA* 5.2 2.9 - - - +
17B TYR* 4.0 16.8 - - + -
20B LEU* 4.1 25.1 - - + -
39B LEU* 4.3 8.5 - - + -
48B VAL* 3.0 25.6 + - + +
49B LEU* 3.5 9.9 - - + +
51B GLY* 1.3 75.0 - - - +
53B LEU* 1.3 60.1 + - - +
55B GLU* 3.7 8.7 + - - +
56B LEU* 3.4 19.8 + - - +
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.8 10.8 - - + -
49B LEU 2.8 14.9 + - - +
50B ASP* 2.8 17.4 + - + +
52B VAL* 1.3 77.6 - - - +
54B MET* 1.3 78.0 + - + +
55B GLU 3.1 0.2 - - - -
56B LEU* 3.1 14.1 + - - +
57B GLN* 3.4 28.5 + - - +
67B VAL* 3.8 40.8 - - + +
68B ILE 4.3 3.1 - - - +
69B ALA* 4.3 17.0 - - + +
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Residues in contact with MET 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ARG* 3.2 48.2 + - - +
232A ALA* 3.4 41.5 - - + +
233A VAL* 4.2 9.2 - - + -
236A ALA* 3.6 6.1 - - + -
50B ASP* 2.7 22.5 + - + +
51B GLY* 3.1 33.6 + - - +
53B LEU* 1.3 79.3 - - + +
55B GLU* 1.3 58.0 + - - +
57B GLN* 3.1 6.3 + - - +
58B ASP* 3.1 26.3 + - - +
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Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A VAL* 3.9 15.9 - - + +
237A ARG* 3.2 19.4 + - - -
241A SER* 4.1 5.6 - - - -
242A ALA 3.0 16.0 + - - -
243A MET* 3.2 11.9 + - + +
244A SER* 2.3 47.5 + - - +
17B TYR* 2.7 26.1 + - - -
51B GLY 3.1 16.8 + - - +
52B VAL* 3.8 8.7 - - - +
54B MET* 1.3 74.6 - - - +
56B LEU* 1.3 64.4 + - - +
57B GLN 3.2 0.4 + - - -
58B ASP* 3.9 3.4 - - - -
59B CYS* 3.3 25.1 + - - -
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A MET* 4.0 15.9 - - + -
20B LEU* 3.4 50.9 - - + +
21B TYR 4.8 0.2 - - - +
24B GLY* 5.1 0.4 - - - -
37B LEU* 3.7 21.5 - - + -
39B LEU* 4.2 8.7 - - + -
52B VAL 3.4 15.3 + - - +
53B LEU 3.1 9.4 + - - +
55B GLU* 1.3 80.3 - - - +
57B GLN* 1.4 61.5 + - - +
59B CYS* 3.5 6.2 + - - -
60B ALA 4.0 1.2 + - - -
61B LEU* 3.6 28.4 + - + +
64B LEU* 3.7 32.2 - - + +
67B VAL* 4.4 13.0 - - + -
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Residues in contact with GLN 57 (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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164A ALA* 3.3 19.4 - - + +
168A LEU* 3.5 40.3 - - + +
229A ARG* 2.4 36.8 + - - +
53B LEU* 3.4 32.9 - - + +
54B MET* 3.1 5.5 + - - +
56B LEU* 1.4 75.7 - - - +
58B ASP* 1.3 55.3 + - - +
59B CYS 3.0 4.9 - - - -
60B ALA* 2.8 26.5 + - - -
61B LEU 5.9 0.2 - - - +
64B LEU* 6.0 0.4 - - - -
67B VAL* 5.0 12.8 - - + +
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Residues in contact with ASP 58 (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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157A LEU* 3.8 12.2 - - + +
160A ASN* 3.5 27.3 + - - +
161A ARG* 2.8 46.1 + - + +
164A ALA* 4.6 3.1 - - - +
229A ARG* 3.1 34.8 + - - +
233A VAL* 4.7 2.8 - - - +
244A SER* 3.8 21.9 + - - +
54B MET 3.1 13.0 + - - +
55B GLU* 4.1 2.2 - - - +
56B LEU 3.4 0.2 - - - -
57B GLN* 1.3 76.1 - - - +
59B CYS* 1.4 59.7 + - - +
60B ALA* 3.2 1.6 - - - -
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Residues in contact with CYS 59 (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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160A ASN* 4.6 1.1 + - - +
243A MET* 4.0 19.3 - - - -
244A SER* 3.8 11.4 - - - -
247A LYS* 2.6 62.5 + - + -
21B TYR* 4.1 9.2 - - - -
55B GLU 3.3 20.1 + - - -
56B LEU 3.7 2.9 - - - +
57B GLN 3.0 1.0 - - - -
58B ASP* 1.4 77.1 - - - +
60B ALA* 1.3 68.5 + - - +
61B LEU* 3.5 24.9 - - + +
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Residues in contact with ALA 60 (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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160A ASN* 3.9 29.6 - - + +
163A LYS* 4.7 8.3 + - + +
164A ALA* 4.8 0.9 - - + -
174A SER* 2.8 33.0 - - - +
247A LYS* 4.3 4.0 + - - +
56B LEU 4.0 0.4 + - - -
57B GLN 2.8 18.5 + - - +
59B CYS* 1.3 83.0 - - - +
61B LEU* 1.3 60.7 + - - +
62B PRO* 3.6 5.7 - - - +
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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
------------------------------------------------------------
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