Contacts of the strand formed by residues 35 - 43 (chain D) in PDB entry 6B0Z
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 VAL 35 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D LYS* 4.2 2.0 - - - -
5D ILE* 3.1 24.7 - - + +
7D GLY* 4.0 6.7 - - - -
31D ILE* 2.9 15.8 + - + +
32D PHE* 3.3 21.3 + - - +
34D TYR* 1.3 83.4 - - - +
36D GLU* 1.3 74.7 + - - +
37D LEU* 3.5 31.4 - - + +
340D LEU* 5.2 2.2 - - + -
352D LEU* 4.2 6.3 - - + -
355D PHE* 3.5 39.3 - - + -
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Residues in contact with GLU 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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4D LYS* 4.2 28.1 + - + +
5D ILE 3.3 5.1 + - - -
6D SER* 3.8 6.0 + - - +
7D GLY 2.9 23.1 + - - -
8D GLY 4.3 0.2 + - - -
32D PHE* 3.5 28.3 - - - +
35D VAL* 1.3 82.3 - - - +
37D LEU* 1.3 82.0 + - - +
39D LEU* 5.0 5.7 - - - +
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Residues in contact with LEU 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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7D GLY* 3.4 29.6 - - - -
8D GLY 3.3 8.7 - - - +
10D VAL* 4.0 20.4 - - + -
31D ILE* 4.5 12.1 - - + -
32D PHE* 4.9 8.5 - - + -
35D VAL* 3.5 15.5 - - + -
36D GLU* 1.3 92.5 + - - +
38D ASP* 1.3 60.7 + - - +
39D LEU* 3.1 38.3 + - + +
336D TRP* 4.2 18.2 - - + -
340D LEU* 4.3 11.4 - - + -
352D LEU* 5.5 0.2 - - + -
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Residues in contact with ASP 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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8D GLY* 2.4 29.7 + - - +
9D SER* 2.9 22.6 + - - +
10D VAL 3.1 15.7 + - - -
37D LEU* 1.3 62.7 - - - -
39D LEU* 1.3 59.6 + - - +
40D HIS* 3.0 39.5 + - - -
67D HIS* 5.1 0.9 + - - -
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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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10D VAL* 3.4 16.8 - - + +
12D GLU* 4.0 28.7 - - + +
27D LYS* 5.2 2.5 - - + +
32D PHE* 4.3 25.6 - - + -
36D GLU* 5.0 4.7 - - - +
37D LEU* 3.1 36.3 + - + +
38D ASP* 1.3 75.2 + - - +
40D HIS* 1.3 61.7 + - - +
41D SER* 3.5 23.6 + - - +
336D TRP* 4.6 6.7 - - + -
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Residues in contact with HIS 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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9D SER* 4.3 2.2 - - - -
10D VAL 3.0 13.0 + - - +
11D VAL* 3.4 16.3 - - + +
12D GLU 2.9 27.1 + - - +
38D ASP* 3.0 46.6 + - - -
39D LEU* 1.3 71.8 - - - +
41D SER* 1.3 61.6 + - - +
42D TYR* 3.8 18.1 - - + +
67D HIS* 3.1 45.4 - + + -
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Residues in contact with SER 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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12D GLU* 3.6 18.7 + - - +
14D GLN* 4.4 9.8 + - - -
39D LEU* 3.5 29.2 + - - +
40D HIS* 1.3 71.9 - - - +
42D TYR* 1.3 70.8 + - - +
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Residues in contact with TYR 42 (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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11D VAL* 4.0 12.1 - - + -
12D GLU 3.0 8.6 + - - +
13D MET* 3.2 5.8 - - + -
14D GLN* 2.9 27.6 + - - +
40D HIS* 3.8 28.0 - - + +
41D SER* 1.3 79.5 - - - +
43D ASP* 1.3 59.7 + - - +
44D LEU* 3.7 16.3 - - + +
56D VAL* 3.9 13.9 - - + -
59D ASP* 4.0 22.3 + - + +
60D ALA* 3.9 17.3 - - + -
63D ALA* 3.4 34.2 - - + +
67D HIS* 5.8 0.2 + - - -
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Residues in contact with ASP 43 (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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14D GLN* 3.6 32.2 - - - +
15D GLY 4.8 1.2 - - - +
20D ARG* 6.1 0.7 - - - -
42D TYR* 1.3 71.7 - - - +
44D LEU* 1.3 59.8 + - - +
45D GLY* 3.2 12.5 + - - -
47D GLU* 2.7 24.9 - - - +
48D ASN* 2.8 46.9 + - - +
56D VAL* 3.7 8.9 - - - +
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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