Contacts of the strand formed by residues 49 - 54 (chain D) in PDB entry 3UYO
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 49 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D THR* 3.3 5.7 - - - -
39D TYR* 2.9 68.3 + - + +
47D PRO 3.8 4.6 + - - +
48D VAL* 1.3 76.4 - - - +
50D GLU* 1.3 65.2 + - - +
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Residues in contact with GLU 50 (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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158A TYR* 2.6 34.5 + - - -
161A SER* 4.6 5.0 + - - -
162A SER* 6.1 0.7 - - - -
239A ARG* 3.0 24.5 + - - -
247A VAL 4.1 11.3 - - - +
36D VAL* 4.3 6.3 - - + +
37D ILE 3.2 11.2 - - - +
38D THR* 3.9 11.2 - - + -
39D TYR* 4.8 0.4 - - - -
48D VAL* 5.4 3.9 - - + +
49D GLN* 1.3 81.4 + - - +
51D PHE* 1.3 69.3 + - - +
52D THR* 5.5 0.5 - - - +
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Residues in contact with PHE 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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36D VAL* 3.5 4.7 - - - +
37D ILE* 2.8 67.7 + - + +
39D TYR* 3.8 26.5 - + - -
50D GLU* 1.3 79.4 - - - +
52D THR* 1.3 76.6 + - - +
53D VAL* 3.9 13.7 - - + -
60D ALA* 4.0 9.9 - - + -
61D THR 3.8 21.5 - - - -
62D ILE* 3.9 15.7 - - + -
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Residues in contact with THR 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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245A TYR 3.8 16.8 + - - -
246A GLY* 4.3 1.0 - - - -
247A VAL 3.5 31.8 + - - +
34D PHE* 4.3 9.8 - - + +
35D TYR 3.1 14.1 - - - +
36D VAL* 4.0 21.5 - - + -
37D ILE* 4.7 0.4 - - - -
50D GLU* 5.5 0.7 - - - +
51D PHE* 1.3 85.0 - - - +
53D VAL* 1.3 71.0 + - - +
54D PRO* 5.0 0.2 - - - +
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Residues in contact with VAL 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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25D TRP* 4.0 25.1 - - + -
34D PHE* 3.3 6.5 - - - +
35D TYR* 2.9 36.3 + - + -
37D ILE* 4.0 7.6 - - + +
51D PHE* 3.9 22.2 - - + -
52D THR* 1.3 80.2 - - - +
54D PRO* 1.4 79.1 - - + +
57D LYS* 3.9 16.8 - - + -
59D THR 4.5 2.5 - - - +
60D ALA* 4.2 12.6 - - + -
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Residues in contact with PRO 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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33D ASP 4.2 4.9 - - - +
34D PHE* 4.4 2.0 - - + -
35D TYR* 3.9 2.3 - - - -
53D VAL* 1.4 95.0 - - + +
55D GLY* 1.3 58.7 + - - +
56D SER* 3.1 20.2 - - - +
57D LYS* 2.9 38.8 + - + +
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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