Contacts of the strand formed by residues 36 - 42 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10H LYS* 3.5 6.0 - - - +
11H ILE* 3.4 25.8 - - + +
13H PHE* 3.9 7.9 - - + -
29H ILE* 4.7 5.6 - - + -
32H HIS 3.5 3.3 + - - +
33H GLY* 2.6 39.5 - - - +
34H ASP 3.5 1.2 - - - -
35H ARG* 1.3 82.6 - - - +
37H GLU* 1.3 60.5 + - - +
309H ILE* 3.8 26.0 - - + -
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Residues in contact with GLU 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H LYS* 3.9 27.2 + - + +
11H ILE 3.0 10.3 + - - +
12H ARG* 3.3 17.2 + - + +
13H PHE* 3.0 26.3 + - - +
29H ILE* 3.9 9.6 - - - -
33H GLY* 4.9 2.9 - - - +
36H ALA* 1.3 78.7 - - - +
38H LEU* 1.3 62.6 + - - +
39H VAL* 3.1 27.3 + - + +
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Residues in contact with LEU 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H PHE* 3.2 27.1 - - + +
14H GLY* 3.9 4.3 - - - -
15H LEU* 4.0 11.4 - - + +
26H ILE* 4.1 29.8 - - + -
29H ILE* 3.8 24.2 - - + +
37H GLU* 1.3 72.2 - - - +
39H VAL* 1.3 57.4 + - - +
40H GLU 3.5 17.0 - - - +
41H ILE* 3.6 23.1 - - + -
56H THR* 4.2 20.5 - - + +
58H ALA* 3.5 13.8 + - + +
77H VAL* 6.1 0.2 - - + -
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Residues in contact with VAL 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H ARG* 3.7 20.9 - - + -
13H PHE 3.0 11.1 + - - +
37H GLU* 3.1 35.4 + - + +
38H LEU* 1.3 73.2 - - - +
40H GLU* 1.3 82.4 + - + +
58H ALA* 3.4 6.8 - - - +
59H ARG* 3.3 17.3 + - - +
72H ASN* 4.0 15.0 - - - +
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Residues in contact with GLU 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H PHE 3.7 2.8 + - - -
14H GLY* 3.1 9.1 - - - -
15H LEU 2.8 22.2 + - - -
38H LEU* 3.5 2.5 - - - +
39H VAL* 1.3 93.4 - - + +
41H ILE* 1.3 69.8 + - - +
58H ALA* 3.5 3.9 - - - +
59H ARG* 3.4 18.4 - - + +
61H PHE* 3.8 18.6 - - + -
67H MET* 4.2 13.8 - - - +
71H GLY* 3.0 11.3 - - - -
72H ASN* 2.6 38.0 + - - -
73H ALA* 3.2 27.5 + - - +
76H LEU* 4.3 1.4 - - - +
97H ARG* 5.5 0.5 + - - -
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Residues in contact with ILE 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H LEU* 3.2 20.4 - - + -
18H CYS* 4.1 6.5 - - - -
26H ILE* 5.7 0.9 - - + -
38H LEU* 3.6 26.2 - - + -
40H GLU* 1.3 80.7 - - - +
42H CYS* 1.3 62.9 + - - +
49H LEU* 4.0 15.6 - - + +
52H ALA* 3.6 15.9 - - + +
53H GLU* 3.3 43.5 - - + +
56H THR* 4.5 4.0 - - + +
58H ALA* 3.9 12.1 - - + +
59H ARG 3.0 10.9 + - - +
60H PRO* 3.5 2.1 - - + +
61H PHE* 2.9 26.3 + - - +
67H MET* 4.3 1.6 - - - -
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Residues in contact with CYS 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H LEU 2.9 10.9 + - - +
16H VAL* 4.1 13.9 - - - -
17H GLY* 2.7 27.5 + - - -
18H CYS* 3.6 5.3 - - - -
41H ILE* 1.3 78.4 - - - +
43H ASP* 1.3 70.3 + - - +
49H LEU* 4.4 0.9 - - - -
61H PHE* 3.2 10.3 - - + +
63H SER* 3.4 39.3 - - - -
64H LEU* 3.7 7.9 - - - -
67H MET* 3.6 22.0 - - + -
500H NAI 4.5 3.8 - - - -
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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