Contacts of the strand formed by residues 55 - 60 (chain B) in PDB entry 3UR9
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 PHE 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ILE* 3.8 42.8 - - + -
27B THR 4.0 1.8 - - - -
29B THR* 3.6 1.3 + - - -
50B HIS 3.8 1.3 - - - +
51B GLN* 3.4 2.9 - - - -
52B ALA 3.0 33.9 + - - +
53B GLY 3.2 1.0 - - - +
54B GLU* 1.3 80.2 - - - +
56B THR* 1.3 68.5 + - - +
57B GLN* 4.4 0.4 - - + -
73B LEU* 4.1 11.4 - - + -
154B CYS 5.5 0.2 - - - -
155B GLY* 4.5 6.7 - - - -
156B VAL* 3.9 17.0 - - + -
170B ALA* 3.5 27.4 - - + -
171B VAL* 3.6 22.4 - - - +
172B GLN* 3.6 46.4 - - + -
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Residues in contact with THR 56 (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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26B ILE* 3.2 8.0 - - - +
27B THR* 2.9 46.2 + - + +
29B THR* 2.8 27.9 + - - -
32B VAL* 4.5 1.1 - - + -
49B ILE* 4.5 0.9 - - + -
50B HIS 3.5 3.1 - - - -
51B GLN* 2.8 34.7 + - + +
55B PHE* 1.3 76.3 - - - +
57B GLN* 1.3 65.3 + - - +
58B PHE* 3.4 35.2 - - + -
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Residues in contact with GLN 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 3.8 28.4 - - + +
25B PHE 3.6 3.8 - - - +
26B ILE* 4.1 5.8 - - + -
48B ALA 3.6 1.4 + - - +
49B ILE* 3.4 6.9 - - - +
50B HIS* 2.8 62.3 + - + +
55B PHE* 4.3 1.0 - - + -
56B THR* 1.3 75.9 - - - +
58B PHE* 1.3 67.9 + - - +
59B ARG* 4.5 26.8 + - - +
73B LEU* 4.1 8.7 - - - +
172B GLN* 2.9 34.5 + - - +
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Residues in contact with PHE 58 (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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12B PHE* 3.9 24.0 - + - -
23B THR 3.6 0.9 - - - +
24B VAL* 3.4 5.0 - - - -
25B PHE* 2.8 49.6 + + - +
27B THR* 3.7 16.2 - - + -
32B VAL* 4.2 13.0 - - + -
39B PHE* 3.6 31.2 - + - -
47B ILE* 3.8 10.3 - - + -
48B ALA 3.6 3.4 - - - -
49B ILE* 3.8 26.2 - - + -
51B GLN* 5.5 0.2 - - - -
56B THR* 3.4 26.0 - - + -
57B GLN* 1.3 77.0 - - - +
59B ARG* 1.3 60.3 + - - +
60B PHE* 3.7 23.3 - + + -
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Residues in contact with ARG 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B THR* 3.4 16.1 + - - +
24B VAL* 3.7 26.5 - - + +
46B SER 4.1 0.3 - - - +
47B ILE* 3.5 4.4 - - - +
48B ALA* 2.8 53.2 + - + +
50B HIS* 6.3 1.5 - - + -
57B GLN* 4.5 21.1 - - - +
58B PHE* 1.3 72.3 - - - +
60B PHE* 1.3 72.4 + - - +
61B SER* 5.0 0.5 + - - -
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Residues in contact with PHE 60 (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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19B TRP* 3.7 24.9 - + - -
23B THR* 2.8 37.5 + - - +
25B PHE* 4.0 5.8 - - + -
39B PHE* 3.8 19.3 - - + -
40B PHE* 3.7 21.1 - + - -
42B GLU* 4.1 9.6 - - + -
46B SER 4.1 2.9 - - - -
47B ILE* 3.6 32.1 - - + -
58B PHE* 3.7 28.0 - + + -
59B ARG* 1.3 84.4 - - - +
61B SER* 1.3 61.1 + - - +
62B LYS* 3.2 18.9 + - + +
64B MET* 3.7 21.5 - - + -
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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