Contacts of the strand formed by residues 33 - 41 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D THR* 3.5 5.0 - - - +
28D ASP* 2.8 29.4 + - + -
31D ALA* 3.2 28.9 - - + +
32D GLY* 1.3 79.0 - - - +
34D GLU* 1.3 66.3 + - - +
69D ARG* 2.5 40.1 + - - +
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Residues in contact with GLU 34 (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 LEU* 3.1 29.0 - - + +
26D GLY 3.6 4.0 - - - +
27D THR* 2.5 31.3 + - - +
33D GLU* 1.3 78.3 - - - +
35D VAL* 1.3 62.8 + - - +
83D GLU* 5.0 0.3 - - - -
84D LEU* 3.4 40.9 + - + +
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Residues in contact with VAL 35 (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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9D TYR* 4.3 3.4 - - + -
25D LEU* 3.8 3.8 - - - +
26D GLY* 2.9 46.7 + - - +
27D THR* 3.8 5.6 - - - +
28D ASP* 4.1 12.8 - - + +
34D GLU* 1.3 78.9 - - - +
36D ALA* 1.3 59.3 + - - +
37D ILE* 4.0 8.3 - - + -
69D ARG* 3.9 35.4 - - - +
81D VAL* 3.6 26.0 - - + -
82D MET 3.4 11.9 - - - +
83D GLU* 4.9 0.9 - - - -
84D LEU* 3.8 11.0 - - - +
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Residues in contact with ALA 36 (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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15D ILE* 5.3 1.3 - - + -
23D ILE* 4.5 15.0 - - + -
24D TYR 3.7 4.0 - - - -
25D LEU* 4.9 0.4 - - - +
35D VAL* 1.3 73.4 - - - +
37D ILE* 1.3 65.7 + - - +
38D LYS 4.2 0.4 - - - -
80D MET 4.1 0.2 - - - +
81D VAL* 3.6 0.3 - - - +
82D MET* 2.7 53.7 + - + +
83D GLU 4.3 3.1 - - - +
84D LEU* 4.0 22.9 - - + +
85D LEU 5.3 1.1 - - - +
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Residues in contact with ILE 37 (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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5D VAL* 3.5 27.1 - - + -
9D TYR* 4.0 9.6 - - + -
10D ARG 4.7 4.0 - - - +
11D LEU* 4.5 13.5 - - + -
22D ASP 3.6 0.3 - - - +
23D ILE* 4.3 2.4 - - - +
24D TYR* 2.5 51.4 + - + +
26D GLY* 4.4 10.3 - - - -
35D VAL* 4.0 11.4 - - + -
36D ALA* 1.3 80.7 - - - +
38D LYS* 1.3 60.9 + - - +
39D LEU* 4.0 11.2 - - + -
79D VAL* 3.5 23.8 - - + -
80D MET 3.8 2.0 - - - -
81D VAL* 3.7 21.3 - - + -
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Residues in contact with LYS 38 (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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17D SER 4.5 3.9 + - - -
22D ASP 3.0 21.5 - - - +
23D ILE* 3.3 30.5 - - + +
36D ALA 4.2 0.8 - - - -
37D ILE* 1.3 73.0 - - - +
39D LEU* 1.3 63.4 + - - +
49D LEU* 3.2 30.0 - - + +
52D GLU* 2.9 34.0 + - - -
56D TYR* 5.8 0.4 + - - -
79D VAL* 3.4 8.8 - - - +
80D MET* 3.1 40.5 + - + +
82D MET* 4.4 13.6 - - + +
149D ASP* 4.4 15.1 + - - +
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Residues in contact with LEU 39 (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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5D VAL* 4.7 4.0 - - + -
11D LEU* 3.7 30.1 - - + -
22D ASP* 2.8 35.8 + - + +
24D TYR* 4.1 25.1 - - + -
37D ILE* 4.0 8.5 - - + -
38D LYS* 1.3 78.3 - - - +
40D GLU* 1.3 62.7 + - - +
49D LEU* 4.7 1.3 - - - -
74D GLU* 5.3 1.3 - - + +
77D TYR* 4.2 36.8 - - + -
78D ASN 3.7 2.9 - - - +
79D VAL* 3.3 37.5 - - + -
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Residues in contact with GLU 40 (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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39D LEU* 1.3 76.5 - - - +
41D CYS* 1.3 76.0 + - + +
47D PRO* 3.6 11.3 - - - +
48D GLN* 2.6 36.2 + - - +
49D LEU* 3.0 35.0 + - + +
50D HIS 5.2 0.7 + - - -
77D TYR* 3.2 6.9 - - - -
78D ASN* 2.5 52.6 + - + +
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Residues in contact with CYS 41 (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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40D GLU* 1.3 91.6 - - - +
42D VAL* 1.3 66.0 + - + +
43D LYS* 4.1 15.2 - - + +
76D ASP 3.8 8.3 - - - +
77D TYR* 4.0 20.2 - - - -
78D ASN* 4.3 1.9 - - - +
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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