Contacts of the strand formed by residues 33 - 41 (chain A) in PDB entry 3UYS
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 33 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A THR* 3.3 3.7 - - - +
28A ASP* 2.6 39.0 + - + +
31A ALA* 2.9 36.5 - - + +
32A GLY* 1.3 75.1 - - - +
34A GLU* 1.3 66.5 + - - +
69A ARG* 2.5 52.2 + - - +
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Residues in contact with GLU 34 (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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10A ARG* 5.9 0.2 + - - -
25A LEU* 4.2 21.7 - - + +
26A GLY 3.3 7.8 - - - +
27A THR* 3.0 25.4 + - - +
32A GLY 5.1 0.7 - - - -
33A GLU* 1.3 82.4 + - - +
35A VAL* 1.3 64.2 + - - +
69A ARG* 4.8 2.1 + - - -
84A LEU* 3.6 35.8 + - + +
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Residues in contact with VAL 35 (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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9A TYR* 4.3 2.5 - - + -
25A LEU* 3.5 4.5 - - - +
26A GLY* 2.5 58.1 + - - +
27A THR* 3.6 9.0 - - - +
28A ASP* 4.1 7.9 - - + +
33A GLU 4.1 7.2 - - - +
34A GLU* 1.3 81.7 - - - +
36A ALA* 1.3 57.8 + - - +
37A ILE* 3.9 10.1 - - + -
69A ARG* 3.9 32.3 - - - +
81A VAL* 3.9 18.8 - - + -
82A MET 3.3 14.1 - - - +
83A GLU* 5.0 0.9 - - - -
84A LEU* 4.1 9.5 - - - +
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Residues in contact with ALA 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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23A ILE* 4.0 19.7 - - + -
24A TYR 3.3 5.2 - - - -
35A VAL* 1.3 72.8 - - - +
37A ILE* 1.3 62.9 + - - +
38A LYS 4.0 0.4 - - - -
80A MET 3.9 0.2 - - - +
81A VAL* 3.6 0.3 - - - +
82A MET* 2.7 57.5 + - + +
83A GLU 4.4 9.2 - - - +
84A LEU* 4.0 19.2 - - + +
85A LEU 5.4 0.7 - - - +
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Residues in contact with ILE 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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5A VAL* 4.2 21.3 - - + -
9A TYR* 4.6 2.9 - - + -
10A ARG 3.6 25.4 - - - +
11A LEU* 4.6 12.3 - - + -
23A ILE* 4.4 0.9 - - - -
24A TYR* 2.7 51.9 + - + +
26A GLY* 4.0 8.5 - - - -
35A VAL* 3.9 16.4 - - + -
36A ALA* 1.3 79.1 - - - +
38A LYS* 1.3 59.1 + - - +
39A LEU* 3.6 24.2 + - + -
79A VAL* 4.6 5.4 - - + -
80A MET 3.5 9.4 - - - +
81A VAL* 4.1 15.5 - - + -
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Residues in contact with LYS 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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21A GLY* 4.2 16.4 - - - +
22A ASP 3.0 20.0 - - - +
23A ILE* 4.1 20.9 - - + +
36A ALA 4.0 1.8 - - - -
37A ILE* 1.3 70.7 - - - +
39A LEU* 1.3 64.6 + - - +
49A LEU* 3.3 21.7 - - + +
52A GLU* 2.6 42.1 + - - -
56A TYR* 4.9 3.4 + - - -
79A VAL* 3.9 0.5 - - - -
80A MET* 3.0 54.0 + - + +
82A MET* 4.7 7.2 - - - +
149A ASP* 4.8 9.1 + - - +
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Residues in contact with LEU 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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11A LEU* 4.3 24.7 - - + -
21A GLY 3.7 17.5 + - - -
22A ASP* 3.4 13.7 + - + +
24A TYR* 4.5 21.7 - - + +
37A ILE* 3.6 17.8 + - + +
38A LYS* 1.3 76.2 - - - +
40A GLU* 1.3 62.5 + - - +
49A LEU* 4.3 0.9 - - - -
74A GLU* 5.2 2.7 - - - +
77A TYR* 4.0 33.4 - - + -
78A ASN 3.7 2.5 - - - +
79A VAL* 3.1 44.4 - - + -
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Residues in contact with GLU 40 (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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21A GLY 4.9 12.2 + - - +
39A LEU* 1.3 79.9 - - - +
41A CYS* 1.3 77.9 + - - +
47A PRO* 4.3 6.8 - - - +
48A GLN* 2.8 32.8 + - - +
49A LEU* 2.9 41.7 + - + +
50A HIS* 4.4 1.4 + - - +
77A TYR* 3.4 5.3 - - - -
78A ASN* 2.9 45.6 + - + +
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Residues in contact with CYS 41 (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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40A GLU* 1.3 87.0 - - + +
42A VAL* 1.3 68.0 + - - +
76A ASP* 3.5 20.0 - - - -
77A TYR* 3.7 19.8 - - + -
78A ASN* 4.8 0.2 - - - +
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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