Contacts of the helix formed by residues 67 - 77 (chain D) 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 ARG 67 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66D CYS* 1.3 79.2 - - + +
68D HIS* 1.3 55.8 + - + +
69D LEU 3.1 4.8 + - - -
70D LEU* 3.4 29.9 - - - +
71D HIS* 3.5 41.4 + - + +
72D LEU* 4.3 2.1 - - - +
74D ILE* 4.3 1.4 - - - +
86D LEU* 3.6 37.7 - - - +
314D LEU 4.9 0.4 + - - -
315D HIS 4.8 7.5 + - - -
316D THR 5.5 1.4 - - - -
317D CYS 4.0 14.8 + - - +
318D ASP* 3.0 16.0 + - - +
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Residues in contact with HIS 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D CYS* 3.1 41.1 - - + +
67D ARG* 1.3 75.8 - - + +
69D LEU* 1.3 74.5 + - + +
72D LEU* 3.4 34.8 - - + +
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Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B ASP* 4.0 23.6 - - - +
66D CYS* 2.8 23.5 + - - +
67D ARG 3.1 1.0 + - - -
68D HIS* 1.3 109.8 - - + +
70D LEU* 1.3 64.4 + - - +
71D HIS 3.6 0.2 - - - -
72D LEU* 3.9 5.0 - - - +
73D ALA* 3.4 20.6 + - - +
150D ARG* 4.2 19.3 - - - +
318D ASP 4.2 4.9 - - - +
319D GLN* 4.9 14.4 - - + -
367D GLY 5.3 0.5 - - - +
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Residues in contact with LEU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D CYS 3.5 3.6 + - - +
67D ARG* 3.4 17.3 - - - +
69D LEU* 1.3 76.7 - - - +
71D HIS* 1.3 61.1 + - - +
73D ALA* 3.1 7.9 + - - +
74D ILE* 2.9 36.8 + - + +
313D ALA 5.1 0.2 - - - +
314D LEU* 3.2 38.1 - - + +
317D CYS 3.3 19.7 - - - +
318D ASP* 3.0 18.6 - - - +
319D GLN* 4.5 10.1 - - + +
320D VAL* 4.9 2.2 - - + -
367D GLY 5.3 1.1 - - - +
368D ILE* 3.1 37.9 - - + +
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Residues in contact with HIS 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ARG* 3.5 39.3 + - + +
70D LEU* 1.3 78.6 - - - +
72D LEU* 1.3 55.1 + - + +
74D ILE* 4.0 13.2 - - + -
75D GLN* 2.7 56.6 + - + +
86D LEU* 4.0 22.3 - - + +
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ARG 4.3 2.7 - - - +
68D HIS* 3.4 41.5 - - + +
69D LEU* 3.8 10.0 + - - +
70D LEU 3.2 0.4 - - - -
71D HIS* 1.3 81.7 - - + +
73D ALA* 1.3 57.5 + - - +
75D GLN* 3.0 9.4 + - - +
76D ARG* 2.9 31.9 + - - +
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Residues in contact with ALA 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B THR* 6.0 3.4 - - + -
69D LEU 3.4 9.8 + - - +
70D LEU* 3.1 9.4 + - - +
72D LEU* 1.3 77.8 - - - +
74D ILE* 1.3 64.0 + - - +
76D ARG* 3.1 26.6 + - - +
77D HIS* 3.8 4.9 + - - +
366D ALA* 3.7 16.8 - - - +
367D GLY* 3.4 28.0 - - - +
368D ILE* 4.1 9.0 - - + +
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Residues in contact with ILE 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ARG* 4.3 0.4 - - - +
70D LEU* 2.9 32.7 + - + +
71D HIS* 3.4 24.7 - - + +
73D ALA* 1.3 76.5 - - - +
75D GLN* 1.3 62.8 + - - +
76D ARG 3.4 0.5 + - - -
77D HIS 3.4 14.0 + - - +
80D PHE* 3.2 24.8 - - - +
81D ARG* 3.4 16.5 + - - +
84D PHE* 3.6 41.3 - - + +
86D LEU* 4.3 11.0 - - + -
368D ILE* 3.8 27.6 - - + -
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Residues in contact with GLN 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D HIS* 2.7 50.0 + - + +
72D LEU* 3.0 8.9 + - - +
74D ILE* 1.3 72.1 - - - +
76D ARG* 1.3 66.3 + - - +
77D HIS 4.0 0.4 - - - -
81D ARG* 3.3 52.3 + - - +
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Residues in contact with ARG 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B HIS 5.4 10.2 + - - -
72D LEU* 2.9 20.4 + - + +
73D ALA* 3.1 17.4 + - - +
75D GLN* 1.3 79.7 - - - +
77D HIS* 1.3 64.2 + - - +
78D PRO* 3.6 2.6 - - - +
81D ARG* 3.7 5.9 + - - -
366D ALA 5.4 3.6 - - - +
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Residues in contact with HIS 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ALA 3.8 4.6 + - - +
74D ILE 3.4 13.7 + - - +
76D ARG* 1.3 82.5 - - - +
78D PRO* 1.3 87.1 - - + +
79D HIS* 3.3 31.8 + + - -
80D PHE* 4.5 15.5 - + + -
81D ARG* 3.6 7.6 + - - +
365D LYS 6.4 0.2 - - - -
366D ALA* 4.7 23.3 - - + -
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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