Contacts of the strand formed by residues 264 - 272 (chain A) in PDB entry 5IZL
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 VAL 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A SER* 3.6 25.8 - - - -
256A VAL 3.3 13.7 - - - +
257A GLU* 4.1 21.5 - - + -
263A VAL* 1.3 82.4 - - - +
265A LYS* 1.3 68.2 + - - +
266A LYS* 5.5 1.7 + - - -
306A PRO* 4.3 15.7 - - + -
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Residues in contact with LYS 265 (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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255A SER* 3.2 3.8 - - - -
256A VAL* 2.9 36.0 + - + +
258A ILE* 4.3 13.2 - - + -
263A VAL* 3.8 28.8 + - + +
264A VAL* 1.3 76.9 + - - +
266A LYS* 1.3 67.1 + - - +
290A VAL* 3.9 23.6 - - + -
291A THR* 3.3 44.6 + - - +
292A GLN 4.3 4.5 + - - -
293A PHE* 3.9 27.8 - - + -
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Residues in contact with LYS 266 (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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253A GLY* 4.4 13.5 - - - +
254A ASP 3.6 3.6 - - - +
255A SER* 4.3 9.0 - - - +
264A VAL 5.5 1.2 + - - -
265A LYS* 1.3 79.9 - - - +
267A VAL* 1.3 60.5 + - - +
268A LYS* 3.3 35.2 + - + +
290A VAL* 3.3 21.7 - - - +
291A THR* 4.2 9.9 + - - -
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Residues in contact with VAL 267 (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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250A ILE* 3.7 26.0 - - + -
251A SER 4.3 2.5 - - - +
252A LEU* 3.6 21.8 - - + +
253A GLY* 3.1 26.5 + - - +
254A ASP 2.8 22.7 + - - +
256A VAL* 4.1 13.7 - - + -
266A LYS* 1.3 71.5 - - - +
268A LYS* 1.3 64.7 + - - +
269A SER 4.3 1.3 - - - +
270A MET* 3.8 22.9 - - + -
288A ILE* 4.2 19.5 - - + -
289A CYS 3.9 3.4 - - - -
290A VAL* 4.2 3.6 - - + -
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Residues in contact with LYS 268 (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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252A LEU* 3.1 18.0 - - - +
266A LYS* 3.9 41.7 - - + +
267A VAL* 1.3 75.6 - - - +
269A SER* 1.3 64.3 + - - +
289A CYS* 3.0 18.4 + - + +
290A VAL* 4.4 8.1 - - - -
291A THR* 3.9 17.5 - - - +
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Residues in contact with SER 269 (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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237A GLN* 5.5 8.7 - - - -
252A LEU* 3.6 5.6 - - - +
267A VAL* 4.3 0.9 - - - +
268A LYS* 1.3 80.2 - - - +
270A MET* 1.3 68.8 + - - +
288A ILE* 3.6 0.2 - - - -
289A CYS* 2.8 46.1 + - - +
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Residues in contact with MET 270 (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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250A ILE* 4.2 24.0 - - - +
251A SER* 3.9 3.6 - - - -
252A LEU* 3.5 23.9 - - + +
267A VAL* 3.8 18.2 - - + -
269A SER* 1.3 81.1 - - - +
271A GLN* 1.3 60.3 + - - +
276A PRO* 3.4 7.8 - - - +
277A ILE* 2.9 49.4 + - + +
278A THR 3.3 37.7 - - - +
279A SER 3.6 4.0 - - - +
280A ALA* 5.0 0.9 - - - -
286A LEU* 4.7 5.2 - - + -
287A GLY 3.5 7.9 - - - +
288A ILE* 4.0 13.7 - - + -
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Residues in contact with GLN 271 (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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270A MET* 1.3 74.6 - - - +
272A MET* 1.3 69.4 - - - +
274A HIS* 3.2 29.9 - - - +
275A MET* 3.1 26.5 - - - +
276A PRO* 3.9 4.9 - - + -
277A ILE* 4.3 2.2 - - - -
286A LEU* 3.4 3.6 - - - +
287A GLY* 3.2 29.8 + - - +
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Residues in contact with MET 272 (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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7A ASN* 6.1 0.7 - - - -
271A GLN* 1.3 79.4 - - - +
273A PHE* 1.3 111.7 + - + +
274A HIS 3.2 1.8 - - - +
275A MET* 2.8 23.8 + - - +
277A ILE* 3.6 36.0 - - + +
279A SER 4.8 3.4 - - - +
284A ASP* 4.0 32.5 - - + +
285A ARG 3.8 23.6 - - - +
286A LEU* 4.1 10.8 - - + +
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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