Contacts of the strand formed by residues 36 - 42 (chain D) in PDB entry 3Q2K
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 ALA 36 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D LYS* 3.8 4.7 - - - +
11D ILE* 3.1 28.0 - - + +
13D PHE* 3.9 22.0 - - + -
29D ILE* 4.1 10.4 - - + +
30D ALA* 6.0 0.2 - - - -
32D HIS 3.2 3.9 + - - +
33D GLY* 3.3 23.7 - - - +
35D ARG* 1.3 82.4 - - - +
37D GLU* 1.3 68.1 + - - +
309D ILE* 4.3 10.1 - - + -
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Residues in contact with GLU 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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10D LYS* 3.7 28.9 + - + +
11D ILE 2.9 9.2 + - - +
12D ARG* 3.7 7.2 - - + +
13D PHE 2.9 23.1 + - - -
29D ILE* 4.0 9.0 - - - -
33D GLY 5.0 1.4 - - - +
36D ALA* 1.3 79.4 - - - +
38D LEU* 1.3 65.2 + - - +
39D VAL* 3.2 17.5 + - + +
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Residues in contact with LEU 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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13D PHE* 3.0 23.3 - - + +
14D GLY 4.1 0.4 - - - -
15D LEU* 3.8 17.5 - - + +
26D ILE* 3.9 31.6 - - + -
29D ILE* 3.9 24.0 - - + +
37D GLU* 1.3 73.8 - - - +
39D VAL* 1.3 60.7 + - - +
40D GLU 3.0 28.0 - - - +
41D ILE* 4.1 15.5 - - + -
56D THR* 4.2 11.6 - - + +
58D ALA* 3.7 16.3 + - + +
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Residues in contact with VAL 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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12D ARG* 3.5 37.2 - - + -
13D PHE 2.5 15.1 + - - +
37D GLU* 3.2 17.9 + - + +
38D LEU* 1.3 75.6 - - - +
40D GLU* 1.3 103.3 + - + +
58D ALA* 3.4 4.7 - - - +
59D ARG* 3.1 18.4 + - - +
72D ASN* 3.7 10.1 - - - +
73D ALA* 4.8 2.2 - - + -
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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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13D PHE 3.5 1.6 + - - -
14D GLY* 3.2 5.4 - - - -
15D LEU 2.8 25.7 + - - -
38D LEU* 3.0 7.6 - - - +
39D VAL* 1.3 103.8 - - + +
41D ILE* 1.3 64.3 + - - +
58D ALA* 3.5 3.0 - - - +
59D ARG* 3.4 9.8 + - + +
61D PHE* 3.7 20.4 - - + -
67D MET* 3.6 22.9 - - - +
71D GLY* 3.6 12.6 - - - -
72D ASN* 2.7 42.7 + - - -
73D ALA* 3.4 17.4 + - + +
97D ARG* 5.6 0.2 + - - -
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Residues in contact with ILE 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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15D LEU* 3.3 10.1 - - + -
18D CYS* 4.0 16.2 - - - -
26D ILE* 6.0 0.2 - - + -
38D LEU* 4.1 17.9 - - + -
40D GLU* 1.3 79.4 - - - +
42D CYS* 1.3 59.7 + - - +
49D LEU* 3.9 12.6 - - + +
52D ALA* 3.6 11.9 - - + -
53D GLU* 3.0 46.7 - - + +
56D THR* 4.1 7.4 - - + +
58D ALA* 4.0 13.9 - - + +
59D ARG 2.9 16.2 + - - +
60D PRO* 3.8 7.2 - - + -
61D PHE* 2.9 26.7 + - - +
67D MET* 4.4 2.9 - - - -
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Residues in contact with CYS 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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15D LEU 2.8 11.1 + - - +
16D VAL* 3.6 7.6 - - - -
17D GLY* 2.7 28.9 + - - -
18D CYS* 3.8 5.0 - - - -
41D ILE* 1.3 72.2 - - - +
43D ASP* 1.3 64.8 + - - +
61D PHE* 3.5 4.7 - - - -
63D SER* 3.4 17.9 - - - -
64D LEU* 3.4 34.8 - - - -
67D MET* 3.3 27.1 - - + -
500D NAI 4.3 12.6 - - - -
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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