Contacts of the strand formed by residues 13 - 20 (chain A) in PDB entry 5KJH
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 ARG 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU 4.4 2.5 - - - +
12A PRO* 1.3 77.6 - - - +
14A LEU* 1.4 65.2 + - - +
15A ARG* 4.2 0.2 - - - +
515A ARG* 3.4 39.3 - - - +
517A LEU* 4.2 15.7 - - - +
549A TYR* 3.3 4.7 - - - -
550A GLN* 2.7 34.7 + - - +
274B GLY 3.7 22.4 - - - +
275B GLU* 3.3 38.6 + - - +
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG* 1.4 74.0 - - - +
15A ARG* 1.3 57.9 + - - +
16A THR 3.7 20.0 - - - +
17A SER* 5.4 0.9 - - - -
517A LEU* 4.4 4.8 - - + +
518A ALA 5.2 8.5 - - - +
519A ILE* 6.1 3.6 - - + -
520A ASP* 5.6 3.1 - - - +
547A LEU* 4.1 20.0 - - + -
548A ILE 4.0 4.5 - - - +
549A TYR* 3.6 36.9 - - + +
272B HIS* 3.5 53.2 - - + +
273B SER* 4.3 4.0 + - - -
274B GLY 5.2 1.0 - - - +
277B GLY* 3.7 25.1 - - - +
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Residues in contact with ARG 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG 3.4 0.8 + - - +
14A LEU* 1.3 73.1 - - - +
16A THR* 1.3 65.7 + - - +
73A THR* 3.2 10.1 + - - -
75A ASP 3.1 21.0 + - - -
76A LYS* 3.2 20.5 + - - +
78A ALA 2.7 23.4 + - - -
80A PRO* 4.0 8.0 - - + +
536A TRP* 4.1 13.0 - - + -
548A ILE 2.9 11.2 + - - +
550A GLN* 3.8 32.1 - - + +
555A GLU* 2.8 28.1 + - - +
271B GLN* 2.8 27.9 + - - +
272B HIS* 2.8 35.3 + - - -
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Residues in contact with THR 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.7 4.0 - - - +
15A ARG* 1.3 77.0 + - - +
17A SER* 1.3 70.7 + - - +
79A ASN* 3.8 11.2 - - - +
80A PRO* 3.2 20.8 - - - +
81A CYS* 4.6 1.8 - - + -
547A LEU 3.7 0.2 - - - -
548A ILE* 2.7 56.9 + - + +
269B PHE* 4.5 7.4 - - + -
270B LYS 3.4 14.1 - - - +
271B GLN* 3.0 28.1 + - - +
272B HIS* 3.7 4.0 - - - -
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Residues in contact with SER 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.9 1.3 - - - -
16A THR* 1.3 80.6 - - - +
18A PHE* 1.3 64.7 + - - +
545A ARG* 5.5 4.0 + - - -
546A ALA 3.2 13.7 - - - -
547A LEU* 3.9 19.5 - - - -
548A ILE* 5.4 0.2 - - - -
269B PHE* 3.5 0.9 - - - -
270B LYS* 2.8 40.4 + - - +
272B HIS* 2.8 26.7 + - - -
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Residues in contact with PHE 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A THR* 5.3 0.2 - - + -
17A SER* 1.3 74.6 - - - +
19A ILE* 1.3 64.0 + - - +
20A PHE* 4.2 8.5 - - + -
40A PHE* 3.8 29.4 - + - -
57A PHE* 4.4 7.0 - + - -
59A ALA* 5.3 0.9 - - + -
66A VAL* 4.7 7.6 - - + -
68A CYS* 4.2 18.2 - - - -
81A CYS* 3.8 22.2 - - - -
83A ILE* 4.9 1.1 - - + -
545A ARG* 3.4 4.2 - - - +
546A ALA* 2.9 52.5 + - + -
548A ILE* 4.0 15.9 - - + -
267B VAL* 3.7 21.8 - - + -
268B LYS 3.1 13.9 - - - +
269B PHE* 3.7 26.9 - + + -
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Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 1.3 78.3 - - - +
20A PHE* 1.3 66.2 + - - +
21A GLN* 3.9 1.0 + - - -
543A GLY 3.4 24.7 - - - +
544A ASN 3.6 2.9 - - - -
545A ARG* 3.9 26.7 - - + +
266B ASP 4.1 0.2 - - - +
267B VAL* 3.4 3.1 - - - -
268B LYS* 3.0 41.7 + - + +
270B LYS* 6.6 0.4 - - - -
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Residues in contact with PHE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 4.1 6.1 - - + -
19A ILE* 1.3 81.3 - - - +
21A GLN* 1.3 73.2 + - - +
22A ASP* 3.6 0.9 + - - -
23A ASP* 4.0 2.9 - - - -
40A PHE* 3.8 32.1 - + + -
61A SER* 3.8 20.0 - - - -
64A HIS* 3.6 31.6 - + + -
66A VAL* 4.0 9.0 - - + -
86A LEU* 3.8 18.4 - - + -
543A GLY 4.0 1.0 - - - +
544A ASN* 2.9 42.0 + - - +
265B MET* 3.6 33.4 - - + -
266B ASP 3.8 3.4 - - - -
267B VAL* 3.7 23.8 - - + -
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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