Contacts of the strand formed by residues 35 - 39 (chain A) in PDB entry 1UFU
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 TYR 35 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A CYS* 3.4 47.0 + - + -
27A GLN* 3.5 5.6 - - - +
28A GLY* 3.1 31.1 + - - -
32A THR* 3.9 24.0 + - - -
33A GLN 3.0 11.1 + - - -
34A GLU* 1.3 74.0 - - - +
36A ARG* 1.3 66.1 + - - +
37A LEU 4.3 0.2 - - - -
55A VAL* 3.2 46.9 + - - +
56A LYS 3.5 18.6 - - - -
57A LYS 4.4 2.2 - - - -
58A GLY* 3.6 12.1 - - - -
60A PHE* 4.2 11.4 - - + -
75A CYS* 4.2 2.5 - - - -
76A TYR 3.9 1.1 - - - -
77A TYR* 4.3 17.3 - + + -
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Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLU* 4.3 13.7 + - - +
35A TYR* 1.3 79.8 - - - +
37A LEU* 1.3 76.3 + - - +
38A TYR* 5.0 6.2 - - - +
60A PHE* 4.8 1.1 - - - -
75A CYS* 3.5 6.4 - - - -
76A TYR* 2.8 79.8 + - + +
78A GLY 4.4 9.4 - - - +
79A SER* 6.0 0.7 - - - +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 3.9 27.8 - - + -
24A LEU* 3.8 24.2 - - + -
36A ARG* 1.3 84.7 + - - +
38A TYR* 1.3 67.4 + - - +
46A TRP* 3.9 11.4 - - + -
47A ILE* 3.9 24.2 - - + +
60A PHE* 3.7 51.6 - - + -
73A TYR* 4.2 10.5 - - + -
74A ARG 3.5 16.8 - - - +
75A CYS* 4.0 7.4 - - + -
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Residues in contact with TYR 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG* 4.8 7.0 - - - +
37A LEU* 1.3 79.8 - - - +
39A ARG* 1.3 74.0 + - - +
40A GLU* 4.6 10.1 - - + -
47A ILE* 4.0 6.5 - - - -
73A TYR* 3.5 6.0 - - - -
74A ARG* 2.9 66.1 + - + -
76A TYR* 3.8 28.7 - + - -
84A ARG* 5.2 1.8 + - - -
87A SER* 3.1 26.8 + - - -
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Residues in contact with ARG 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 1.3 83.4 - - - +
40A GLU* 1.3 75.5 + - - +
42A LYS* 2.6 46.1 + - - +
43A THR* 3.2 28.3 + - - +
44A ALA* 3.7 20.1 - - + +
45A PRO* 4.7 2.8 - - - +
47A ILE* 4.3 2.8 - - - +
68A GLU* 2.7 34.3 + - - +
70A ALA 2.9 20.6 + - - -
71A GLY* 3.9 4.5 - - - -
72A ARG 3.3 18.4 - - - +
73A TYR* 3.8 33.6 + - + +
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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