Contacts of the helix formed by residues 48 - 57 (chain F) in PDB entry 2M6X
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 TRP 48 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45F LEU* 5.0 14.4 - - + +
47F VAL* 1.3 77.4 - - - +
49F PRO* 1.3 85.6 - - + +
50F LEU 3.2 3.7 + - - +
51F LEU* 3.6 31.3 + - + +
52F LEU* 4.2 29.3 + - + +
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Residues in contact with PRO 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 5.0 11.7 - - + -
23B LEU* 4.9 13.9 - - + -
45F LEU* 3.7 51.1 - - + +
46F GLY 4.6 1.3 - - - +
47F VAL* 3.9 1.8 - - - +
48F TRP* 1.3 103.5 - - + +
50F LEU* 1.3 67.8 + - + +
52F LEU* 3.1 21.0 + - + +
53F VAL* 3.3 14.5 + - - +
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Residues in contact with LEU 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 4.1 27.4 - - + -
23B LEU* 4.8 5.1 - - + +
46F GLY 5.4 3.4 - - - +
47F VAL* 5.3 4.5 - - - -
48F TRP 4.9 4.5 - - - +
49F PRO* 1.3 78.8 - - + +
51F LEU* 1.3 69.8 + - + +
53F VAL* 2.9 23.8 + - + +
54F ARG* 2.7 42.6 + - + +
57F ARG* 5.0 11.2 - - + +
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Residues in contact with LEU 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F VAL 4.7 3.8 - - - +
48F TRP* 3.6 41.3 - - + +
49F PRO 3.2 0.6 - - - -
50F LEU* 1.3 82.0 - - + +
52F LEU* 1.3 70.7 + - + +
54F ARG* 2.9 28.7 - - - +
55F LEU* 3.5 9.3 - - - +
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Residues in contact with LEU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B VAL* 6.5 0.7 - - + -
30B TRP* 4.6 24.2 - - + -
48F TRP* 4.2 33.2 - - + +
49F PRO* 3.1 13.1 + - + +
51F LEU* 1.3 79.5 - - + +
53F VAL* 1.3 63.7 + - + +
55F LEU* 3.1 26.3 + - - +
56F LEU* 4.0 1.7 + - - +
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Residues in contact with VAL 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLY 4.4 14.8 - - - +
19B PHE* 4.5 9.9 - - - +
22B GLY 5.6 0.2 - - - -
23B LEU* 3.4 37.2 - - + +
26B VAL* 6.5 0.9 - - + -
49F PRO 3.3 15.7 - - - +
50F LEU* 2.9 26.9 + - + +
52F LEU* 1.3 75.0 - - + +
54F ARG* 1.3 65.9 + - - +
56F LEU* 2.8 23.8 + - + +
57F ARG* 2.9 24.7 + - + +
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Residues in contact with ARG 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F LEU* 2.7 20.0 + - + +
51F LEU* 2.9 22.6 + - - +
53F VAL* 1.3 76.7 - - - +
55F LEU* 1.3 61.1 + - + +
57F ARG* 3.0 14.4 + - + +
58F PRO* 2.7 28.7 - - + +
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Residues in contact with LEU 55 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51F LEU 3.5 17.5 - - - +
52F LEU* 3.4 13.2 - - - +
53F VAL 3.1 0.6 - - - -
54F ARG* 1.3 82.8 - - + +
56F LEU* 1.3 56.2 + - - +
58F PRO* 3.0 23.2 - - - +
59F HIS 4.6 0.5 + - - -
60F ARG* 5.8 2.3 + - - -
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Residues in contact with LEU 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLY* 3.6 19.4 - - - +
21B TRP* 5.9 1.1 - - + -
22B GLY* 3.4 38.1 - - - +
25B VAL* 5.3 4.0 - - + -
26B VAL* 5.4 11.2 - - + -
15C GLY* 5.4 11.0 - - - +
52F LEU 4.0 0.9 + - - +
53F VAL* 2.8 19.4 + - + +
55F LEU* 1.3 80.3 - - - +
57F ARG* 1.3 63.2 + - - +
58F PRO* 3.4 0.4 - - - -
59F HIS* 3.2 27.6 + - + +
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Residues in contact with ARG 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B HIS* 4.3 14.3 + - - -
18B GLY* 5.1 5.6 - - - +
19B PHE* 2.8 61.7 - - - +
50F LEU* 5.0 12.6 - - + +
53F VAL* 2.9 25.5 + - + +
54F ARG* 3.3 21.3 - - + +
56F LEU* 1.3 77.0 - - - +
58F PRO* 1.3 65.5 - - + +
59F HIS* 3.3 4.7 + - - +
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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
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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