Contacts of the strand formed by residues 24 - 31 (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 GLU 24 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C GLY* 5.9 2.0 - - - -
150C PRO* 6.5 0.7 - - + -
152C GLN* 3.4 28.1 + - - +
164C VAL* 3.8 20.0 - - - +
165C PRO* 3.9 15.5 - - - +
22D LYS* 4.4 21.4 - - + +
23D TRP* 1.3 76.5 - - - +
25D CYS* 1.3 61.5 + - - +
56D TYR* 3.2 11.3 - - - -
57D TYR* 2.9 65.2 + - + +
58D SER* 6.0 0.8 - - - -
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Residues in contact with CYS 25 (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* 4.2 11.3 - - - -
148C HIS* 3.5 34.7 + - - +
152C GLN* 5.0 4.9 + - - +
4D GLU* 5.5 1.6 - - - +
24D GLU* 1.3 80.0 - - - +
26D GLU* 1.3 62.8 - - - +
27D SER 3.9 0.3 + - - -
54D TYR* 3.6 41.1 - - - -
55D THR 3.5 4.3 - - - -
56D TYR* 3.6 28.0 - - + -
57D TYR* 3.9 4.9 + - - -
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Residues in contact with GLU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C TYR* 2.6 37.5 + - + -
167C PRO* 3.3 8.1 - - - +
168C PRO* 3.8 21.5 - - + +
169C SER* 2.7 44.6 + - - -
270C SER* 4.3 2.3 + - - -
271C PRO* 4.2 6.1 - - - +
25D CYS* 1.3 74.8 - - - +
27D SER* 1.3 62.1 + - - +
28D ILE* 4.0 22.7 + - + +
53D THR* 3.3 4.3 + - - +
54D TYR* 3.4 0.7 - - - -
55D THR* 2.7 44.9 + - - +
57D TYR* 4.0 0.8 - - + -
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Residues in contact with SER 27 (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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144C GLN* 4.3 7.3 - - - +
145C ASP* 4.7 12.6 + - - +
147C TYR* 5.2 2.6 - - - -
148C HIS* 4.5 6.2 + - - -
214C ALA* 3.3 34.2 - - - +
215C ASN* 3.4 4.6 + - - +
25D CYS 3.9 1.4 + - - -
26D GLU* 1.3 76.5 - - - +
28D ILE* 1.3 67.4 + - - +
52D GLN* 3.2 20.6 + - - -
53D THR 3.1 8.7 + - - -
54D TYR* 3.5 10.3 - - - -
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Residues in contact with ILE 28 (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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144C GLN* 3.6 19.1 - - + +
147C TYR* 5.7 1.6 - - + +
158C PHE* 5.6 2.5 - - + -
169C SER* 4.7 0.2 - - - +
268C HIS* 3.5 44.2 - - + +
270C SER* 4.2 13.9 - - - +
26D GLU* 4.0 24.2 - - + +
27D SER* 1.3 83.1 + - - +
29D GLU* 1.3 76.6 + - - +
30D GLU* 4.6 6.3 - - + -
52D GLN* 3.4 5.2 - - - -
53D THR* 2.8 48.4 + - - +
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Residues in contact with GLU 29 (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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144C GLN* 2.8 36.3 + - - +
215C ASN* 5.1 2.5 - - - +
218C LYS* 2.6 41.0 + - - +
248C TYR* 3.5 31.2 - - + +
268C HIS* 5.6 0.2 - - - -
28D ILE* 1.3 73.9 - - - +
30D GLU* 1.3 68.2 + - - +
50D ILE* 3.4 32.9 - - + +
51D LEU 3.2 5.8 - - - +
52D GLN* 3.0 24.1 - - - +
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Residues in contact with GLU 30 (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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246C GLY* 3.2 13.2 - - - -
247C SER* 2.9 41.7 + - - -
248C TYR 5.8 0.2 - - - +
268C HIS* 4.4 5.6 + - + +
273C SER* 4.8 9.0 - - - +
28D ILE* 3.8 8.5 + - + +
29D GLU* 1.3 78.4 - - - +
31D ILE* 1.3 89.2 + - - +
34D ASP* 3.9 23.7 - - + +
35D ILE* 3.4 29.7 - - + +
50D ILE* 4.2 6.3 - - - +
51D LEU* 2.7 38.6 + - - +
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Residues in contact with ILE 31 (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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247C SER* 3.2 26.2 + - - +
251C LYS* 4.1 14.1 - - - +
30D GLU* 1.3 92.6 + - - +
32D ALA* 1.3 68.8 + - - +
33D ASP* 3.3 22.7 - - + +
34D ASP* 3.1 22.6 + - + +
35D ILE* 3.8 4.4 + - - +
48D ASN* 3.6 27.6 - - - +
49D LYS 3.4 11.2 - - - +
50D ILE* 4.1 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