Contacts of the strand formed by residues 11 - 16 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9K ARG* 4.3 2.4 + - - +
10K LYS* 1.3 71.2 - - - +
12K ARG* 1.3 65.5 + - - +
13K PHE* 4.3 11.7 - - + -
35K ARG 3.0 15.0 + - - +
36K ALA* 3.1 16.7 - - + +
37K GLU* 3.0 25.5 + - - +
74K ASP* 3.6 20.4 - - + +
75K ALA 5.2 0.2 - - - +
309K ILE* 4.6 11.2 - - + -
312K LEU* 3.5 51.4 - - + +
313K ARG* 3.8 25.4 - - + -
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Residues in contact with ARG 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K ARG* 3.3 39.7 - - + +
10K LYS 3.9 7.2 - - - +
11K ILE* 1.3 75.0 - - - +
13K PHE* 1.3 62.3 + - - +
37K GLU* 3.7 26.2 - - + +
39K VAL* 3.6 29.6 - - + +
72K ASN* 2.9 36.5 + - - +
73K ALA* 3.5 1.4 - - - +
74K ASP* 2.7 49.4 + - - +
75K ALA 3.6 0.9 + - - -
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Residues in contact with PHE 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K ILE* 3.8 5.6 + - + -
12K ARG* 1.3 73.5 - - - +
14K GLY* 1.3 59.4 + - - +
29K ILE* 4.0 20.9 - - + -
36K ALA* 4.0 27.6 - - + -
37K GLU 3.0 11.7 + - - +
38K LEU* 3.0 31.7 - - + +
39K VAL* 3.4 16.6 + - - +
40K GLU 3.5 2.8 + - - -
73K ALA* 4.0 2.2 - - - -
75K ALA* 3.3 34.5 - - + -
77K VAL* 4.3 13.0 - - + -
100K VAL* 4.7 3.8 - - + -
305K TYR* 3.9 29.4 - + - -
308K VAL* 4.1 12.3 - - + -
309K ILE* 4.3 10.8 - - + -
312K LEU* 4.0 18.4 - - + -
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Residues in contact with GLY 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K PHE* 1.3 75.3 - - - +
15K LEU* 1.3 55.2 + - - -
38K LEU* 4.1 1.3 - - - -
40K GLU* 3.4 13.2 - - - -
67K MET* 5.0 0.4 - - - -
73K ALA* 3.5 10.0 - - - +
75K ALA 2.8 10.6 + - - +
76K LEU* 3.5 20.9 - - - -
77K VAL* 2.6 36.0 + - - +
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Residues in contact with LEU 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K GLY* 1.3 73.9 - - - -
16K VAL* 1.3 64.5 + - - +
17K GLY 3.8 6.7 - - - +
18K CYS* 4.0 17.3 - - - -
22K SER* 3.6 31.4 - - - +
25K HIS* 4.2 18.6 - - + -
26K ILE* 4.3 15.7 - - + -
29K ILE* 5.7 1.1 - - + -
38K LEU* 4.3 10.3 - - + -
40K GLU 3.0 12.3 + - - +
41K ILE* 3.4 8.5 - - + -
42K CYS* 2.9 29.9 + - - +
67K MET* 4.0 1.8 - - - +
76K LEU* 4.2 0.6 - - - +
77K VAL* 3.6 31.2 - - + -
79K ALA* 4.5 9.4 - - + -
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Residues in contact with VAL 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K LEU* 1.3 73.6 - - - +
17K GLY* 1.3 61.4 + - - +
42K CYS* 3.9 14.6 - - + -
64K LEU* 4.1 13.5 - - + -
67K MET* 3.4 25.6 - - + -
76K LEU* 4.1 7.2 - - + -
77K VAL 2.9 20.8 + - - +
78K LEU* 3.6 17.7 - - + -
79K ALA 2.8 27.9 + - - -
80K THR* 3.2 13.5 - - + +
88K GLN* 4.0 12.3 - - - +
500K NAI 3.8 20.6 - - + +
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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