Contacts of the strand formed by residues 11 - 16 (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 ILE 11 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9H ARG* 4.9 5.2 - - - +
10H LYS* 1.3 73.6 - - - +
12H ARG* 1.3 67.6 + - - +
13H PHE* 3.4 28.5 + - + -
35H ARG 3.0 16.1 + - - +
36H ALA* 3.4 4.8 - - + +
37H GLU* 3.0 27.7 + - - +
74H ASP* 3.7 13.5 - - + +
75H ALA* 5.1 0.4 - - + -
309H ILE* 4.4 17.9 - - + -
312H LEU* 3.7 41.1 - - + +
313H ARG* 4.7 16.4 - - + -
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Residues in contact with ARG 12 (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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9H ARG* 3.0 50.6 - - - +
10H LYS 3.4 1.5 + - - +
11H ILE* 1.3 73.4 - - - +
13H PHE* 1.3 60.3 + - - +
37H GLU* 3.3 28.5 + - - +
39H VAL* 3.7 15.7 - - + -
72H ASN* 3.0 47.0 + - - +
73H ALA* 3.4 14.1 - - - -
74H ASP* 2.5 48.1 + - - +
75H ALA 3.3 6.2 + - - -
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Residues in contact with PHE 13 (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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11H ILE* 3.4 30.3 + - + -
12H ARG* 1.3 73.0 - - - +
14H GLY* 1.3 61.1 + - - +
29H ILE* 4.1 26.7 - - + -
36H ALA* 3.9 7.0 - - + -
37H GLU 3.0 13.5 + - - +
38H LEU* 3.2 5.8 - - + +
39H VAL* 3.0 26.2 + - - +
40H GLU 3.7 1.6 + - - -
73H ALA* 3.7 2.9 - - - -
75H ALA* 3.3 31.9 - - + -
77H VAL* 4.2 9.4 - - + -
100H VAL* 4.4 5.6 - - + -
305H TYR* 3.9 21.5 - + - -
308H VAL* 3.8 28.9 - - + -
309H ILE* 3.7 27.8 - - + -
312H LEU* 4.5 1.1 - - + -
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Residues in contact with GLY 14 (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* 1.3 74.8 - - - +
15H LEU* 1.3 59.3 + - - -
38H LEU* 3.9 2.0 - - - -
40H GLU* 3.1 21.8 - - - -
67H MET* 4.7 0.7 - - - -
73H ALA* 3.4 3.8 - - - +
75H ALA 2.8 9.8 + - - +
76H LEU* 3.5 19.0 - - - -
77H VAL* 2.9 29.5 + - - +
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Residues in contact with LEU 15 (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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14H GLY* 1.3 72.9 - - - -
16H VAL* 1.3 60.8 + - - +
17H GLY 3.6 24.2 - - - +
18H CYS* 4.0 17.3 - - - -
22H SER* 3.8 18.2 - - - -
25H HIS* 4.2 15.7 - - + -
26H ILE* 4.5 15.9 - - + -
29H ILE* 6.3 0.9 - - + -
38H LEU* 4.1 9.6 - - + -
40H GLU 2.8 6.9 + - - -
41H ILE* 3.2 18.8 - - + -
42H CYS* 2.9 28.1 + - - +
67H MET* 4.0 3.8 - - - +
77H VAL* 3.7 30.5 - - + +
79H ALA* 4.2 8.3 - - + -
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Residues in contact with VAL 16 (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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14H GLY 4.1 0.6 + - - -
15H LEU* 1.3 73.2 - - - +
17H GLY* 1.3 65.7 + - - +
42H CYS* 3.9 15.9 - - - -
64H LEU* 4.5 12.3 - - + -
67H MET* 4.3 10.7 - - + +
76H LEU* 5.5 1.3 - - + -
77H VAL 2.9 26.8 + - - +
78H LEU* 3.0 36.3 - - + -
79H ALA* 2.9 21.9 + - - +
80H THR* 3.8 5.3 + - + -
88H GLN* 4.1 13.0 - - - +
500H NAI 3.8 21.5 - - + -
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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