Contacts of the helix formed by residues 69 - 77 (chain B) in PDB entry 6APL
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 69 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B CYS 4.9 1.3 - - - +
67B ARG 2.9 4.9 + - - -
68B HIS* 1.3 97.5 - - + +
70B LEU* 1.3 67.3 + - - +
71B HIS 3.6 0.7 - - - -
72B LEU* 3.7 3.4 + - - +
73B ALA* 3.3 21.1 + - - +
148B CYS* 4.6 4.3 - - - -
150B ARG* 3.3 39.5 - - - +
318B ASP* 3.6 10.1 - - + +
319B GLN* 3.6 29.4 - - + +
367B GLY 5.1 1.7 - - - +
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Residues in contact with LEU 70 (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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67B ARG* 3.5 15.5 + - + +
69B LEU* 1.3 78.9 - - + +
71B HIS* 1.3 59.9 + - - +
73B ALA* 3.2 7.8 + - - +
74B ILE* 2.9 39.6 + - + +
314B LEU* 3.2 41.3 - - + +
317B CYS 3.3 17.5 - - - +
318B ASP* 3.1 20.9 + - - +
319B GLN* 4.0 15.0 - - - +
320B VAL* 4.1 7.4 - - + +
367B GLY 5.5 1.1 - - - +
368B ILE* 3.2 30.4 - - + +
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Residues in contact with HIS 71 (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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67B ARG* 3.6 42.0 + - + +
70B LEU* 1.3 78.6 - - - +
72B LEU* 1.3 56.6 + - + +
74B ILE* 3.0 21.4 + - + +
75B GLN* 2.7 51.3 + - + +
81B ARG* 5.9 2.6 + - - -
86B LEU* 4.5 19.8 - - + +
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Residues in contact with LEU 72 (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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67B ARG 3.3 16.4 + - - +
68B HIS* 3.5 32.1 - - + +
69B LEU 3.7 7.2 + - - +
70B LEU 3.2 0.6 - - - -
71B HIS* 1.3 80.2 - - + +
73B ALA* 1.3 57.4 + - - +
75B GLN* 3.6 3.9 + - - +
76B ARG* 3.0 28.6 + - - +
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Residues in contact with ALA 73 (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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69B LEU 3.3 10.5 + - - +
70B LEU 3.2 6.7 + - - +
72B LEU* 1.3 75.6 - - - +
74B ILE* 1.3 65.1 + - - +
76B ARG* 3.6 5.6 - - - +
77B HIS* 3.2 29.3 + - + +
366B ALA 3.8 12.8 - - - +
367B GLY* 3.8 13.7 - - - +
368B ILE* 3.4 19.6 - - + +
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Residues in contact with ILE 74 (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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67B ARG* 4.7 6.1 - - - +
70B LEU* 2.9 38.9 + - + +
71B HIS* 3.4 22.4 - - + +
73B ALA* 1.3 77.1 - - - +
75B GLN* 1.3 63.8 + - - +
76B ARG 3.3 0.2 + - - -
77B HIS* 3.0 20.5 - - - +
80B PHE* 3.9 20.7 - - - +
81B ARG* 3.7 10.7 + - - +
84B PHE* 4.1 39.9 - - + -
86B LEU* 5.3 4.7 - - + -
314B LEU 5.3 0.9 - - - +
368B ILE* 3.5 21.5 - - + -
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Residues in contact with GLN 75 (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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71B HIS* 2.7 35.3 + - + +
72B LEU* 4.2 4.3 - - - +
74B ILE* 1.3 74.4 - - - +
76B ARG* 1.3 63.8 + - - +
81B ARG* 3.3 54.4 + - - +
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Residues in contact with ARG 76 (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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72B LEU 3.0 19.8 + - - +
73B ALA* 3.6 8.5 - - - +
74B ILE 3.1 0.2 - - - -
75B GLN* 1.3 80.1 - - - +
77B HIS* 1.3 104.5 + - - +
78B PRO* 3.5 25.2 - - - +
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Residues in contact with HIS 77 (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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73B ALA* 3.2 20.7 + - + +
74B ILE 3.0 16.6 - - - +
76B ARG* 1.3 116.4 + - + +
78B PRO* 1.3 68.8 - - + +
79B HIS* 4.6 4.9 - - + +
80B PHE* 4.9 10.1 - - + -
81B ARG* 3.2 11.7 + - - +
365B LYS 4.4 3.2 + - - -
366B ALA* 3.0 52.4 + - + -
368B ILE* 5.5 0.4 - - + -
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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