Contacts of the strand formed by residues 50 - 57 (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 ILE 50 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251C LYS* 4.0 17.9 - - - +
29D GLU* 3.4 42.4 - - + +
30D GLU* 3.5 9.4 - - - +
31D ILE* 4.1 19.7 - - + +
48D ASN 4.0 2.2 + - - +
49D LYS* 1.3 71.1 - - - +
51D LEU* 1.3 65.3 + - - +
52D GLN 4.4 0.2 + - - -
73D TYR* 3.5 27.3 - - + -
74D GLN* 4.9 2.3 + - - +
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Residues in contact with LEU 51 (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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28D ILE 3.6 1.2 - - - +
29D GLU* 3.2 7.6 - - - -
30D GLU 2.7 36.3 + - - +
32D ALA* 3.7 24.0 - - + -
35D ILE* 4.9 7.0 - - + -
36D LEU* 4.2 17.0 - - + -
46D LEU* 4.0 21.5 - - + -
49D LYS* 3.9 11.0 - - + +
50D ILE* 1.3 84.2 - - - +
52D GLN* 1.3 62.7 + - - +
53D THR* 4.2 11.1 - - + +
71D LEU* 4.5 19.5 - - + -
72D TYR 3.3 15.9 - - - +
73D TYR* 4.0 13.9 - - + -
78D ILE* 4.5 4.5 - - + -
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Residues in contact with GLN 52 (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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215C ASN* 2.9 43.4 + - - +
218C LYS* 5.2 2.9 - - - +
900C MG 4.1 0.4 - - - -
27D SER* 3.2 15.0 + - - -
28D ILE 3.4 25.9 - - - +
29D GLU* 3.0 28.2 - - - +
50D ILE 4.4 0.4 + - - -
51D LEU* 1.3 73.4 - - - +
53D THR* 1.3 61.6 + - - +
54D TYR* 3.7 21.9 - - + +
70D ILE 3.9 0.5 - - - +
71D LEU* 3.5 3.5 - - - +
72D TYR* 2.8 43.5 + - + +
73D TYR* 5.1 0.2 - - - +
74D GLN 4.9 8.0 - - - +
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Residues in contact with THR 53 (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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270C SER* 5.1 0.9 + - - -
272C LEU* 3.5 20.4 - - + +
26D GLU 3.3 0.7 + - - +
27D SER* 3.1 11.1 + - - -
28D ILE* 2.8 54.8 + - - +
30D GLU 5.1 0.2 - - - +
35D ILE* 3.7 27.3 - - + +
51D LEU* 4.2 10.8 - - + +
52D GLN* 1.3 78.0 - - - +
54D TYR* 1.3 63.2 + - - +
55D THR* 4.7 2.1 + - - -
70D ILE 3.8 2.7 - - - -
71D LEU* 3.5 17.9 - - + -
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Residues in contact with TYR 54 (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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148C HIS* 5.3 0.4 - + - -
214C ALA* 3.5 29.0 + - + +
215C ASN* 3.8 6.8 + - - -
4D GLU* 6.1 0.2 - - - -
25D CYS* 3.6 25.8 - - - -
26D GLU 3.4 2.5 - - - -
27D SER* 3.5 13.0 - - - -
52D GLN* 3.7 27.6 - - + +
53D THR* 1.3 73.5 - - - +
55D THR* 1.3 62.8 + - - +
56D TYR* 3.8 18.4 - - + +
69D PHE* 2.9 8.5 - - - +
70D ILE* 2.9 47.0 + - + +
72D TYR* 3.5 34.2 - + - +
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Residues in contact with THR 55 (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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168C PRO* 4.1 6.1 - - + -
270C SER* 4.4 5.2 + - - -
271C PRO* 4.1 17.5 - - + -
272C LEU* 3.6 28.7 - - + +
25D CYS* 3.5 1.3 - - - -
26D GLU* 2.7 49.4 + - - +
53D THR* 4.7 2.1 + - - -
54D TYR* 1.3 74.9 - - - +
56D TYR* 1.3 65.5 + - - +
57D TYR* 4.0 2.1 - - - -
67D TYR* 3.8 31.9 - - + -
68D PRO 3.4 5.8 - - - +
69D PHE* 4.2 2.3 - - + +
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Residues in contact with TYR 56 (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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4D GLU* 3.2 42.9 + - + +
7D LEU* 4.7 4.9 - - + -
23D TRP* 3.7 36.8 - + + -
24D GLU 3.2 16.4 - - - +
25D CYS* 3.6 23.4 - - + -
54D TYR* 3.8 28.7 - - + +
55D THR* 1.3 71.2 - - - +
57D TYR* 1.3 64.1 + - - +
61D LEU* 3.8 2.6 - - - +
67D TYR* 3.7 11.6 - - - -
68D PRO* 2.9 44.4 + - + +
70D ILE* 3.8 27.8 - - + +
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Residues in contact with TYR 57 (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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147C TYR* 4.5 2.8 - - - -
152C GLN* 2.8 26.9 + - - -
160C VAL* 5.0 0.3 - - - +
165C PRO* 4.0 11.9 + - + -
166C PRO 3.8 4.5 - - - -
167C PRO* 3.8 27.6 - - + +
168C PRO* 3.4 28.3 - - + -
23D TRP* 3.6 2.4 - - - -
24D GLU* 2.9 53.1 + - + +
25D CYS 3.7 25.4 - - - -
26D GLU* 4.0 2.7 - - + -
55D THR 4.0 4.5 - - - -
56D TYR* 1.3 77.4 - - - +
58D SER* 1.3 64.6 + - - +
61D LEU* 3.7 11.0 - - - -
62D HIS* 3.4 32.8 - + + -
67D TYR* 4.2 4.7 - - + -
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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