Contacts of the strand formed by residues 24 - 31 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A GLY* 5.9 1.6 - - - -
152A GLN* 3.3 28.8 + - + +
164A VAL* 3.6 25.6 - - - +
165A PRO* 3.9 15.5 - - - +
22B LYS* 4.2 22.8 - - + +
23B TRP* 1.3 74.8 - - - +
25B CYS* 1.3 62.5 + - - +
56B TYR* 3.3 11.9 - - - -
57B TYR* 2.9 58.5 + - + -
58B SER* 5.8 0.5 - - - -
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Residues in contact with CYS 25 (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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147A TYR* 4.2 11.6 - - - -
148A HIS* 3.8 31.9 + - - +
152A GLN* 4.8 5.4 + - - +
4B GLU* 5.6 1.3 - - - +
24B GLU* 1.3 78.4 - - - +
26B GLU* 1.3 66.9 + - - +
27B SER 4.1 0.2 + - - -
54B TYR* 3.5 44.6 - - - -
55B THR 3.5 4.0 - - - -
56B TYR* 3.9 22.2 - - + -
57B TYR* 3.7 7.6 + - - -
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Residues in contact with GLU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A TYR* 2.8 36.5 + - + +
167A PRO* 3.2 9.7 - - - +
168A PRO* 3.7 20.4 - - + +
169A SER* 2.9 42.0 + - - -
270A SER* 4.3 5.9 + - - -
271A PRO* 4.2 6.2 - - - +
25B CYS* 1.3 74.6 - - - +
27B SER* 1.3 64.5 + - - +
28B ILE* 4.1 16.9 + - + +
53B THR* 3.2 5.4 + - - +
54B TYR* 3.3 1.0 - - - -
55B THR* 2.7 48.1 + - - +
57B TYR* 3.9 0.9 - - + -
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Residues in contact with SER 27 (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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144A GLN* 4.5 6.2 - - - +
145A ASP* 4.4 14.0 + - - +
147A TYR* 5.2 2.6 - - - -
148A HIS* 4.3 8.0 - - - -
214A ALA* 3.2 34.3 - - - +
215A ASN* 3.5 2.3 + - - +
25B CYS 4.1 0.6 + - - -
26B GLU* 1.3 79.0 - - - +
28B ILE* 1.3 65.5 + - - +
52B GLN* 3.2 19.8 + - - -
53B THR 3.0 8.9 + - - -
54B TYR* 3.6 11.6 - - - -
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Residues in contact with ILE 28 (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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144A GLN* 3.7 20.2 - - + +
147A TYR* 5.8 1.1 - - - +
158A PHE* 5.6 2.7 - - + -
169A SER* 4.7 0.4 - - - +
268A HIS* 3.4 45.5 - - + +
270A SER* 4.2 13.0 - - - +
26B GLU* 4.1 23.1 - - + +
27B SER* 1.3 82.7 + - - +
29B GLU* 1.3 73.2 + - - +
30B GLU* 4.8 5.8 - - + -
52B GLN* 3.5 4.5 - - - -
53B THR* 2.9 49.1 + - + +
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Residues in contact with GLU 29 (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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144A GLN* 2.8 34.4 + - - +
215A ASN* 4.9 2.7 - - - +
218A LYS* 2.6 38.6 + - - +
248A TYR* 3.4 31.5 - - + +
268A HIS* 5.6 0.2 - - - -
28B ILE* 1.3 75.2 - - - +
30B GLU* 1.3 67.6 + - - +
50B ILE* 3.6 33.1 - - + +
51B LEU 3.3 5.2 - - - +
52B GLN* 3.2 23.4 - - - +
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Residues in contact with GLU 30 (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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246A GLY* 3.3 11.6 - - - -
247A SER* 2.7 43.6 + - - -
248A TYR 4.6 0.2 + - - -
268A HIS* 4.4 6.5 + - + +
273A SER* 4.7 8.3 - - - +
28B ILE* 3.9 6.2 + - + -
29B GLU* 1.3 78.4 - - - +
31B ILE* 1.3 87.6 + - - +
34B ASP* 3.9 22.8 - - + +
35B ILE* 3.2 30.2 - - + +
50B ILE* 4.2 5.8 - - - +
51B LEU* 2.7 41.7 + - - +
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Residues in contact with ILE 31 (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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247A SER* 3.5 18.6 + - - +
251A LYS* 4.4 13.0 - - - +
30B GLU* 1.3 97.5 + - - +
32B ALA* 1.3 69.9 + - - +
33B ASP* 3.3 22.9 - - + +
34B ASP* 3.1 23.7 + - + +
35B ILE* 3.8 3.8 + - - +
48B ASN* 3.5 28.0 - - - +
49B LYS 3.2 12.1 - - - +
50B ILE* 4.1 21.0 - - + +
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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