Contacts of the helix formed by residues 50 - 55 (chain B) in PDB entry 6CM9
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 50 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.8 38.8 - - + +
18B LEU* 3.7 33.7 - - + -
19B LYS* 4.2 29.2 - - + -
22B LEU* 5.0 5.2 - - + -
37B VAL* 4.5 7.4 - - + -
47B VAL* 3.2 29.7 + - + +
49B ALA* 1.3 81.2 - - + +
51B PHE* 1.3 63.4 + - - +
52B PRO* 3.7 2.0 - - - -
53B ASP* 3.7 10.3 + - + +
54B VAL* 3.5 24.0 + - + +
72B TYR* 3.7 5.2 - - - +
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Residues in contact with PHE 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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48B SER* 3.5 15.8 + - - +
49B ALA 3.2 1.2 - - - -
50B LEU* 1.3 78.0 - - - +
52B PRO* 1.3 69.9 - - + +
53B ASP 2.9 7.0 + - - -
54B VAL* 3.3 9.7 + - - +
55B VAL* 3.3 22.8 - - + +
72B TYR* 3.6 23.5 + + + -
73B LEU* 3.6 39.3 - - + -
76B TYR* 3.4 28.5 - - + -
77B ALA* 5.2 1.3 - - + -
80B GLN* 3.7 13.9 - - + +
83B MET* 3.6 45.1 - - + -
84B ALA* 3.9 16.6 - - + -
86B MET* 6.4 0.2 - - + -
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Residues in contact with PRO 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA 4.3 7.9 - - - +
50B LEU 4.0 1.6 - - - -
51B PHE* 1.3 100.5 - - + +
53B ASP* 1.3 67.3 + - - +
54B VAL 3.7 0.2 - - - -
55B VAL* 4.3 10.5 - - + +
56B ASN* 3.4 20.8 + - - +
80B GLN* 4.9 7.4 - - - +
83B MET* 4.5 11.4 - - + +
86B MET* 6.5 0.9 - - + -
80C HIS* 3.4 46.5 - - + +
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Residues in contact with ASP 53 (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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19B LYS* 3.3 32.7 + - + +
22B LEU* 3.4 30.1 - - + +
23B ASN* 4.7 13.9 + - - +
49B ALA 5.5 0.7 - - - +
50B LEU* 4.2 8.3 - - - +
51B PHE 2.9 1.6 + - - -
52B PRO* 1.3 89.0 - - - +
54B VAL* 1.3 63.7 + - - +
55B VAL 3.3 1.1 - - - -
56B ASN* 3.9 19.2 + - - +
57B CYS 4.1 1.4 + - - -
80C HIS* 3.5 16.1 - - - +
83C GLN* 4.1 15.5 + - - +
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 3.7 24.0 - - + -
34B VAL* 4.6 10.3 - - + -
37B VAL* 4.4 28.0 - - + -
50B LEU* 3.5 15.2 + - + +
51B PHE 3.3 8.7 + - - +
53B ASP* 1.3 75.9 - - - +
55B VAL* 1.3 67.3 + - + +
56B ASN 3.2 0.7 - - - -
57B CYS* 3.0 29.7 + - - +
69B VAL* 4.1 10.8 - - + +
72B TYR* 3.5 34.1 - - + -
73B LEU* 5.9 0.2 - - + -
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Residues in contact with VAL 55 (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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51B PHE* 3.3 30.7 + - + +
52B PRO* 4.5 7.6 - - + -
53B ASP 3.3 0.6 - - - -
54B VAL* 1.3 82.6 - - + +
56B ASN* 1.3 65.2 + - - +
57B CYS 3.2 0.2 - - - -
58B MET* 3.2 21.2 - - + +
69B VAL* 4.9 1.8 - - + -
73B LEU* 3.7 33.0 - - + -
86B MET* 3.3 31.4 - - + +
87B ALA* 4.8 4.3 - - + -
51C PHE* 3.2 22.6 - - + -
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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