Contacts of the strand formed by residues 264 - 273 (chain B) 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 THR 264 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLN* 4.1 4.3 + - - +
88A ARG* 5.0 0.7 + - - -
252B ILE* 5.5 0.4 - - + -
258B ARG* 3.2 35.5 + - - +
259B PRO* 3.6 25.4 + - + +
262B VAL* 3.6 5.9 + - - +
263B PRO* 1.3 78.5 + - - +
265B MET* 1.3 75.7 + - - +
287B GLN* 3.6 34.1 - - + +
288B TYR 3.3 13.2 + - - +
289B PRO* 4.6 2.4 - - - +
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Residues in contact with MET 265 (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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20A PHE* 3.6 24.2 - - + -
21A GLN* 3.3 35.7 - - + +
22A ASP 3.9 8.3 - - - +
23A ASP* 3.7 30.5 - - + -
64A HIS* 3.7 14.6 - - + +
86A LEU* 3.8 9.0 - - + -
88A ARG* 3.5 18.2 - - - +
264B THR* 1.3 78.2 - - - +
266B ASP* 1.3 64.0 + - - +
267B VAL* 4.9 0.3 - - - +
288B TYR* 2.8 38.4 + - - +
290B VAL* 3.5 20.6 - - + -
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Residues in contact with ASP 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE 4.1 0.2 - - - +
20A PHE* 3.9 0.9 - - - -
21A GLN* 2.7 53.2 + - + +
258B ARG* 2.9 29.3 + - - -
265B MET* 1.3 72.2 - - - +
267B VAL* 1.3 61.9 + - - +
285B ARG* 2.8 44.3 + - + -
286B PHE 3.3 4.0 - - - +
287B GLN* 3.5 15.2 - - - +
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Residues in contact with VAL 267 (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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18A PHE* 3.7 32.8 - - + -
19A ILE 3.4 5.2 - - - +
20A PHE* 3.7 24.5 - - + -
66A VAL* 5.6 0.2 - - + -
83A ILE* 3.7 18.6 - - + -
86A LEU* 6.1 0.7 - - + -
265B MET 4.9 0.4 - - - +
266B ASP* 1.3 80.3 - - - +
268B LYS* 1.3 63.3 + - - +
269B PHE* 3.7 24.5 + - + -
284B ARG 3.9 1.4 - - - +
285B ARG* 3.3 4.3 - - - -
286B PHE* 2.8 31.8 + - - +
288B TYR* 3.8 20.9 - - + -
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Residues in contact with LYS 268 (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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18A PHE* 3.1 5.9 - - - -
19A ILE* 3.0 43.0 + - + +
267B VAL* 1.3 73.1 - - - +
269B PHE* 1.3 63.6 + - - +
270B LYS* 4.9 11.9 - - + +
282B SER* 3.1 32.3 + - - +
283B GLY* 4.4 7.9 - - - -
284B ARG 3.5 14.4 - - - +
285B ARG* 4.0 15.9 - - + +
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Residues in contact with PHE 269 (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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16A THR* 4.5 5.8 - - + -
17A SER 3.5 2.0 - - - -
18A PHE* 3.7 32.5 - + + -
79A ASN* 3.4 35.0 - - - +
81A CYS* 4.0 18.4 - - + -
83A ILE* 3.8 12.3 - - + -
267B VAL* 3.7 21.3 - - + -
268B LYS* 1.3 74.7 - - - +
270B LYS* 1.4 61.3 + - - +
271B GLN* 4.1 10.1 + - - +
283B GLY* 3.1 4.7 - - - -
284B ARG* 2.8 38.6 + - + +
286B PHE* 3.7 26.7 - + + -
288B TYR* 3.3 27.6 - - - -
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Residues in contact with LYS 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 3.4 8.7 - - - +
17A SER* 2.8 38.2 + - - +
19A ILE* 6.6 0.2 - - - -
520A ASP* 6.3 1.4 - - - +
268B LYS* 4.2 11.6 + - + +
269B PHE* 1.4 75.4 - - - +
271B GLN* 1.3 63.8 + - - +
272B HIS* 3.7 19.6 - - + +
279B SER* 3.3 28.7 + - - +
281B ASN 5.1 0.4 + - - -
282B SER* 3.6 20.2 - - - +
283B GLY* 4.0 13.9 - - - -
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Residues in contact with GLN 271 (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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15A ARG* 2.8 30.0 + - - +
16A THR* 3.0 18.2 + - - +
76A LYS 3.9 9.2 - - - +
77A ASP* 3.6 23.1 - - - +
78A ALA 3.3 12.0 - - - +
79A ASN* 3.2 31.6 + - - +
80A PRO* 3.3 1.7 - - - +
269B PHE* 4.1 9.1 + - - +
270B LYS* 1.3 86.4 + - - +
272B HIS* 1.3 56.7 + - - +
279B SER* 3.5 6.1 + - - -
280B ARG* 2.8 41.8 + - + -
281B ASN* 5.3 11.4 + - - +
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Residues in contact with HIS 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 3.5 43.7 - - + +
15A ARG* 2.8 29.3 + - - +
16A THR* 3.7 17.7 - - - -
17A SER* 2.8 28.7 + - - -
76A LYS 4.9 0.3 - - - +
520A ASP* 5.2 6.3 - - - -
270B LYS* 3.7 25.9 + - + +
271B GLN* 1.3 75.0 - - - +
273B SER* 1.3 64.1 + - - +
277B GLY 2.9 25.3 + - - +
278B LYS 3.4 4.9 - - - -
279B SER* 3.7 18.9 - - - -
280B ARG* 4.2 3.4 - - - -
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Residues in contact with SER 273 (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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14A LEU 4.6 3.1 - - - -
76A LYS* 4.7 12.8 - - - -
272B HIS* 1.3 75.8 - - - +
274B GLY* 1.3 64.4 + - - +
276B TYR 5.1 0.2 + - - -
277B GLY* 4.8 1.1 - - - -
278B LYS* 3.2 30.7 + - - +
280B ARG* 3.1 41.1 + - - +
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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