Contacts of the helix formed by residues 67 - 77 (chain M) in PDB entry 6AH0
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 67 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63M LEU 3.7 6.5 + - - -
64M GLU* 3.0 15.8 + - - +
66M ILE* 1.3 77.4 - - - +
68M HIS* 1.3 62.7 + - - +
69M LEU 3.2 0.6 + - - -
70M PRO* 3.8 8.3 - - - +
71M LEU* 4.1 4.3 + - - -
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Residues in contact with HIS 68 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242L SER 4.8 2.2 + - - -
243L LYS* 3.7 35.6 - - - +
64M GLU 4.5 2.8 + - - -
65M ILE 5.5 0.4 - - - -
66M ILE 3.2 2.0 - - - -
67M LEU* 1.3 77.5 - - - +
69M LEU* 1.3 59.5 + - - +
71M LEU* 3.0 5.2 + - - +
72M LEU* 2.9 26.2 + - - -
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Residues in contact with LEU 69 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66M ILE 3.3 10.1 + - - -
67M LEU 3.2 1.4 - - - -
68M HIS* 1.3 76.3 - - - +
70M PRO* 1.3 57.9 - - - +
72M LEU* 3.3 1.9 + - - +
73M CYS* 2.8 27.7 + - - -
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Residues in contact with PRO 70 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66M ILE 4.5 1.8 - - - -
67M LEU* 3.8 7.3 - - - +
68M HIS 3.4 0.6 - - - -
69M LEU* 1.3 75.2 - - - +
71M LEU* 1.3 56.1 + - - +
73M CYS* 3.8 2.0 - - - +
74M GLU* 2.9 24.9 + - - -
80M TYR* 6.6 0.4 - - - -
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Residues in contact with LEU 71 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67M LEU 4.1 4.6 + - - -
68M HIS* 3.0 9.7 + - - +
70M PRO* 1.3 75.6 - - - +
72M LEU* 1.3 63.9 + - - +
74M GLU* 3.1 2.6 + - - +
75M ASP* 3.1 19.1 + - - -
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Residues in contact with LEU 72 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46M LEU* 6.5 0.9 - - - -
68M HIS 2.9 12.9 + - - -
69M LEU* 3.8 2.9 - - - +
71M LEU* 1.3 75.5 - - - +
73M CYS* 1.3 60.3 + - - +
75M ASP* 3.3 2.7 + - - +
76M LYS* 2.9 19.6 + - - -
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Residues in contact with CYS 73 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69M LEU 2.8 20.6 + - - -
70M PRO* 3.8 2.5 - - - -
72M LEU* 1.3 69.8 - - - +
74M GLU* 1.3 59.3 + - - +
76M LYS* 3.1 2.2 + - - +
77M ASN* 2.7 28.6 + - - -
78M VAL* 3.1 26.5 + - - +
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Residues in contact with GLU 74 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70M PRO 2.9 20.5 + - - -
71M LEU 3.1 2.2 + - - -
73M CYS* 1.3 72.5 - - - +
75M ASP* 1.3 64.1 + - - +
77M ASN* 3.4 9.7 + - - +
78M VAL 5.4 0.2 - - - -
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Residues in contact with ASP 75 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71M LEU 3.1 11.5 + - - -
72M LEU* 3.7 3.4 - - - +
74M GLU* 1.3 78.5 - - - +
76M LYS* 1.3 58.0 + - - +
77M ASN* 3.3 0.7 + - - -
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Residues in contact with LYS 76 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72M LEU 2.9 14.3 + - - -
73M CYS* 3.7 2.0 - - - +
75M ASP* 1.3 74.0 - - - +
77M ASN* 1.3 64.1 + - - +
78M VAL* 3.4 2.6 + - - -
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Residues in contact with ASN 77 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73M CYS 2.7 13.0 + - - -
74M GLU* 3.4 7.1 + - - +
75M ASP 3.2 5.1 + - - -
76M LYS* 1.3 74.8 - - - +
78M VAL* 1.3 55.8 + - - +
79M PRO 4.3 0.5 - - - -
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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