Contacts of the strand formed by residues 33 - 38 (chain D) in PDB entry 6BA5
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 ILE 33 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D CYS* 5.2 2.5 - - + +
23D ALA* 6.0 0.9 - - + -
31D TYR* 3.6 17.6 + - + +
32D PRO* 1.3 82.0 - - - +
34D SER* 1.3 73.8 + - - +
35D TRP* 3.8 21.5 - - + +
49D PHE* 3.2 3.5 - - - -
50D ILE* 3.0 33.3 + - - +
70D ARG* 4.9 0.4 - - - +
75D VAL* 3.7 31.2 - - + -
92D CYS* 4.0 12.8 - - + -
93D ALA 3.5 11.4 - - - +
94D ARG* 3.8 10.8 - - + -
95D GLY 4.0 0.7 - - - -
5F GLU* 3.9 28.5 - - - +
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Residues in contact with SER 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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33D ILE* 1.3 75.3 - - - +
35D TRP* 1.3 64.4 + - - +
36D VAL* 4.9 1.1 - - - -
46D TRP* 3.3 27.4 + - - -
48D GLY 3.3 5.6 - - - -
49D PHE* 3.3 9.4 - - - +
92D CYS* 3.3 4.9 - - - -
93D ALA* 2.8 35.8 + - - +
95D GLY 2.8 21.1 + - - -
96D TYR* 3.7 3.3 - - - -
103D PHE* 3.5 19.7 - - - -
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Residues in contact with TRP 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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19D LEU* 3.9 28.3 - - + -
20D THR 4.1 4.5 - - - -
21D CYS* 3.5 21.5 - - + -
33D ILE* 3.8 4.6 - - + +
34D SER* 1.3 74.2 - - - +
36D VAL* 1.3 61.8 + - - +
46D TRP* 3.9 1.6 - - - -
47D ILE* 2.8 42.4 + - + +
48D GLY 3.0 10.1 + - - +
68D ILE* 3.7 30.7 - - + +
75D VAL* 3.7 41.0 - - + +
77D LEU* 3.6 43.1 - - + +
90D TYR* 4.9 1.1 - - + -
91D PHE 3.3 21.3 - - - -
92D CYS* 3.8 16.6 - - + -
7F GLU* 3.6 22.0 - - - -
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Residues in contact with VAL 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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102C PHE* 3.8 25.6 - - + -
34D SER* 4.9 2.2 - - - +
35D TRP* 1.3 81.0 - - - +
37D ARG* 1.3 72.1 + - - +
44D LEU* 4.1 17.3 - - + -
45D GLU 3.4 14.4 - - - +
46D TRP* 4.0 19.3 - - + -
47D ILE* 4.2 3.6 - - - +
90D TYR* 3.6 1.6 - - - +
91D PHE* 2.8 35.4 + - + +
93D ALA* 5.3 1.3 - - + -
103D PHE* 4.7 7.9 - - + -
106D TRP* 4.0 27.8 - - + -
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Residues in contact with ARG 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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36D VAL* 1.3 77.6 - - - +
38D GLN* 1.3 64.0 + - - +
39D ALA 5.4 0.4 - - - +
44D LEU* 3.5 1.6 - - - -
45D GLU* 2.8 71.2 + - + +
47D ILE* 4.1 9.4 - - + +
61D TRP* 3.5 27.3 - - - -
65D ARG* 5.1 0.8 - - - +
66D PHE* 3.9 7.9 - - - -
85D ASP* 4.1 13.5 + - - +
86D ASP* 2.8 33.1 + - - +
88D ALA* 4.0 10.1 - - + -
89D THR 3.2 11.2 - - - +
90D TYR* 3.1 43.7 + - + -
91D PHE* 5.0 0.7 - - - -
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Residues in contact with GLN 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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39C GLN* 2.9 43.4 + - - -
88C TYR* 3.2 12.5 + - - -
37D ARG* 1.3 77.4 - - - +
39D ALA* 1.3 69.5 + - - +
40D PRO* 3.7 0.7 - - - +
41D GLY 5.7 0.4 - - - +
42D LYS 3.1 28.0 + - - +
43D GLY 3.6 10.2 - - - +
44D LEU* 3.7 15.2 - - + +
88D ALA* 3.6 2.7 - - - -
89D THR* 2.9 38.1 + - - +
91D PHE* 3.8 13.0 - - + -
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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