Contacts of the strand formed by residues 19 - 25 (chain B) in PDB entry 3K3B
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 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B GLY 3.6 6.7 + - - +
18B ASN* 1.3 77.1 - - + +
20B GLN* 1.3 59.8 + - - +
21B VAL* 4.4 7.2 - - + -
299B ILE* 3.8 34.3 - - + +
302B LEU* 3.8 41.5 - - + +
303B VAL* 4.0 22.9 - - + -
324B LEU* 5.8 0.9 - - - +
330B THR* 3.1 20.6 - - - +
332B ILE* 4.1 14.6 - - + -
357B LYS* 2.8 29.0 + - + +
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Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LYS* 3.3 44.7 - - - +
18B ASN 4.3 2.9 - - - +
19B ILE* 1.3 72.7 - - - +
21B VAL* 1.3 62.6 + - - +
22B VAL* 4.1 6.3 - - + -
69B ASP* 3.0 27.7 + - + +
70B MET* 4.2 16.3 - - + +
89B ILE* 6.5 0.7 - - + -
329B ARG* 6.2 2.9 - - - +
330B THR 2.8 9.2 + - - +
331B SER* 3.3 14.3 + - - +
332B ILE* 3.0 26.0 + - - +
357B LYS* 3.7 10.6 + - - -
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Residues in contact with VAL 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE* 4.4 3.6 - - + -
20B GLN* 1.3 76.3 - - - +
22B VAL* 1.3 66.0 + - - +
68B PHE* 3.1 28.7 - - + +
69B ASP* 2.8 35.3 + - - +
332B ILE* 3.6 33.2 - - + +
334B ALA* 5.3 1.3 - - + -
353B ALA* 3.9 25.4 - - + +
356B ALA* 4.7 0.9 - - + -
357B LYS* 3.5 35.9 - - + +
359B ILE* 5.4 0.7 - - + -
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLN* 4.9 2.2 - - + -
21B VAL* 1.3 80.1 - - - +
23B VAL* 1.3 65.6 + - - +
69B ASP* 4.8 1.3 - - + -
70B MET* 3.1 49.8 - - + +
72B PHE* 3.5 26.0 - - + -
85B VAL* 4.2 7.0 - - + -
331B SER* 4.7 8.7 - - - +
332B ILE 3.0 8.2 + - - +
333B ILE* 3.6 34.1 - - + -
334B ALA* 2.9 25.6 + - - +
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B VAL* 1.3 78.7 - - - +
24B ARG* 1.3 61.0 + - - +
25B CYS* 4.3 2.5 - - + +
43B CYS* 5.2 0.4 - - - -
50B VAL* 4.6 6.5 - - + -
68B PHE* 3.5 42.4 - - + -
70B MET 3.1 6.7 + - - -
71B VAL* 4.6 10.3 - - + -
72B PHE* 2.8 37.6 + - - +
334B ALA* 3.2 19.7 - - + +
336B ILE* 3.8 32.1 - - + -
350B LEU* 3.8 12.3 - - + -
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Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B VAL 4.3 0.6 - - - -
23B VAL* 1.3 73.7 - - - +
25B CYS* 1.3 68.9 + - - +
26B ARG 3.9 0.7 + - - -
72B PHE* 3.7 18.6 - - + -
73B GLY 4.8 0.9 - - - +
76B THR* 3.2 26.5 + - - +
77B LYS* 3.7 11.5 - - - +
78B GLN* 2.9 29.4 + - - +
81B VAL* 3.6 23.1 - - + +
109B THR 4.8 0.7 - - - +
113B PHE* 3.7 12.9 - - - -
114B THR* 2.9 36.3 + - - +
333B ILE* 4.0 17.6 - - + +
334B ALA 3.0 9.2 + - - -
335B THR* 3.1 11.5 - - + +
336B ILE 3.0 21.2 + - - -
371B ADP 3.4 24.2 + - - +
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Residues in contact with CYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B VAL* 4.0 1.0 - - - +
24B ARG* 1.3 78.0 - - - +
26B ARG* 1.3 74.6 + - - +
41B VAL* 4.3 10.5 - - - -
43B CYS* 3.7 24.9 - - - -
72B PHE 3.1 8.3 + - - +
73B GLY 3.2 5.5 - - - +
74B ALA* 3.1 30.2 - - - +
336B ILE* 3.4 19.7 - - + +
337B SER 4.1 1.8 - - - -
338B PRO* 3.8 31.0 - - - -
371B ADP 4.6 1.2 + - - -
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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