Contacts of the strand formed by residues 76 - 83 (chain D) in PDB entry 5AYR
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 GLN 76 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B LYS* 3.6 34.2 - - + +
72D TYR* 3.2 3.2 - - - -
73D TYR* 2.7 53.7 + - + +
74D GLN* 3.4 0.8 - - + +
75D LYS* 1.3 79.8 - - - +
77D LEU* 1.3 68.4 + - - +
78D ILE* 3.2 10.7 + - - +
95D HIS* 3.2 35.0 + - + -
97D THR* 3.9 19.9 + - - +
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Residues in contact with LEU 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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3D LEU* 3.9 19.3 - - + -
70D ILE* 3.6 31.4 - - + -
71D LEU 3.6 3.4 - - - +
72D TYR* 3.5 24.4 - - + +
75D LYS 3.6 2.2 + - - -
76D GLN* 1.3 77.3 - - - +
78D ILE* 1.3 72.6 + - - +
79D ALA 3.8 7.9 - - - +
80D ILE* 4.0 16.4 - - + -
93D TYR* 3.9 29.9 + - + +
95D HIS* 4.0 5.0 - - - +
105D ARG* 5.0 10.3 - - - +
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Residues in contact with ILE 78 (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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36D LEU* 4.8 2.5 - - + -
46D LEU* 4.1 17.3 - - + -
51D LEU* 4.5 9.2 - - + -
71D LEU* 2.6 25.7 + - + +
72D TYR 3.9 1.6 - - - -
73D TYR* 3.5 22.4 - - + +
76D GLN* 3.4 29.8 - - - +
77D LEU* 1.3 82.0 - - - +
79D ALA* 1.3 65.4 + - + +
93D TYR* 3.9 4.9 - - - -
94D LEU* 3.2 5.4 - - + +
95D HIS* 2.9 52.3 + - + +
97D THR* 4.1 13.9 - - + +
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Residues in contact with ALA 79 (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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69D PHE* 4.3 1.8 - - + -
70D ILE* 3.2 11.0 - - - +
71D LEU* 2.8 56.5 + - + -
77D LEU* 3.8 3.2 - - - +
78D ILE* 1.3 82.4 - - + +
80D ILE* 1.3 65.4 + - - +
91D PHE* 4.2 9.2 - - + -
93D TYR* 3.1 15.4 - - - +
94D LEU* 4.0 12.8 - - + -
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Residues in contact with ILE 80 (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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3D LEU* 4.0 24.2 - - + -
7D LEU* 3.9 31.9 - - + -
69D PHE* 3.6 8.5 - - - +
70D ILE* 4.5 5.4 - - + +
77D LEU* 4.0 26.2 - - + -
79D ALA* 1.3 79.9 - - - +
81D GLY* 1.3 57.6 + - - +
91D PHE* 3.5 4.3 - - - +
92D LEU* 2.7 40.8 + - + -
93D TYR* 3.1 28.4 + - + +
105D ARG* 4.0 18.2 - - + -
108D LEU* 4.4 9.0 - - + -
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Residues in contact with GLY 81 (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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7D LEU* 4.2 6.7 - - - +
68D PRO* 3.3 5.0 - - - +
69D PHE* 2.9 37.0 + - - +
80D ILE* 1.3 79.9 - - - +
82D TYR* 1.3 68.8 + - - +
90D ASP 3.0 15.3 - - - -
91D PHE* 4.1 1.3 - - - -
92D LEU* 4.2 5.4 - - - -
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Residues in contact with TYR 82 (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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7D LEU* 6.0 0.2 - - + -
10D TYR* 4.6 10.8 + + - -
11D ILE* 3.7 22.9 - - + -
14D LEU* 3.6 29.8 - - + +
15D PHE* 3.8 23.0 - + - -
66D ILE* 4.4 4.9 - - + -
67D TYR 3.3 12.8 - - - +
68D PRO* 3.8 9.2 - - + -
69D PHE* 3.3 8.4 - - - -
81D GLY* 1.3 77.5 - - - +
83D ILE* 1.3 70.4 + - - +
84D ASP* 4.3 14.6 - - + -
88D ASP 3.7 0.5 - - - +
89D MET* 3.7 0.3 - - - -
90D ASP* 2.9 64.6 + - + -
92D LEU* 5.2 7.6 - - + -
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Residues in contact with ILE 83 (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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271C PRO* 4.2 23.8 - - + +
272C LEU* 3.1 36.1 - - + -
65D ASN 3.6 1.0 - - - +
66D ILE* 3.3 6.8 - - - +
67D TYR* 2.8 52.4 + - + +
69D PHE* 4.1 1.8 - - + -
82D TYR* 1.3 76.7 - - - +
84D ASP* 1.3 74.6 + - - +
87D HIS* 3.7 38.6 - - + +
88D ASP 3.5 4.0 - - - +
89D MET* 4.0 22.0 - - + -
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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