Contacts of the strand formed by residues 263 - 272 (chain B) 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 263 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B GLU* 3.7 2.9 - - - +
258B ILE* 3.1 28.9 + - + +
261B LEU* 2.8 38.8 + - + +
262B LYS* 1.3 81.9 - - - +
264B VAL* 1.3 72.3 + - - +
265B LYS* 4.5 20.6 - - + -
293B PHE* 6.4 0.4 - - + -
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Residues in contact with VAL 264 (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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255B SER* 3.7 26.9 - - - +
256B VAL 3.4 10.5 - - - +
257B GLU* 3.8 24.0 - - + -
258B ILE 4.8 0.2 - - - +
262B LYS 5.6 0.7 - - - +
263B VAL* 1.3 82.6 - - - +
265B LYS* 1.3 72.1 + - - +
306B PRO* 4.1 13.5 - - + -
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Residues in contact with LYS 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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255B SER* 3.2 4.3 - - - -
256B VAL* 2.8 39.4 + - + +
258B ILE* 4.4 19.3 - - + -
261B LEU* 6.2 0.4 - - - -
263B VAL* 4.5 15.9 - - + -
264B VAL* 1.3 84.6 - - - +
266B LYS* 1.3 62.2 + - - +
290B VAL* 3.9 24.2 - - + -
291B THR* 2.9 43.6 + - - +
292B GLN 3.4 12.5 + - - -
293B PHE* 4.3 17.7 - - - +
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Residues in contact with LYS 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B GLY* 4.0 13.2 - - - +
254B ASP 3.6 4.7 - - - -
255B SER* 4.3 7.4 - - - +
265B LYS* 1.3 74.2 - - - +
267B VAL* 1.3 66.0 + - - +
268B LYS* 3.4 2.6 + - - +
290B VAL* 3.1 19.5 - - - +
291B THR* 4.6 8.8 + - + +
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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
----------------------------------------------------------
250B ILE* 3.6 26.7 - - + -
251B SER 3.9 14.8 - - - +
252B LEU* 4.1 7.9 - - + +
253B GLY* 3.3 18.9 + - - +
254B ASP 3.0 20.9 + - - +
256B VAL* 3.7 13.7 - - + -
266B LYS* 1.3 72.2 - - - +
268B LYS* 1.3 63.3 + - - +
269B SER 4.2 1.3 - - - +
270B MET* 3.8 21.8 - - + -
288B ILE* 3.7 23.8 - - + -
290B VAL* 3.9 6.1 - - + -
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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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237B GLN 5.8 1.8 - - - +
252B LEU* 3.0 15.0 - - - +
266B LYS 3.4 3.7 + - - +
267B VAL* 1.3 72.6 - - - +
269B SER* 1.3 63.2 + - - +
289B CYS* 2.9 26.7 + - + +
290B VAL* 4.4 6.7 - - - -
291B THR* 5.4 2.9 - - + +
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Residues in contact with SER 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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237B GLN* 5.7 0.3 + - - -
252B LEU* 3.6 6.5 - - - -
267B VAL 3.8 0.4 - - - -
268B LYS* 1.3 80.8 - - - +
270B MET* 1.3 67.7 + - - +
271B GLN* 5.5 6.6 - - - +
276B PRO* 6.5 0.9 - - - -
287B GLY 4.0 0.2 - - - +
288B ILE* 3.3 5.0 - - - +
289B CYS* 2.8 50.4 + - - +
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Residues in contact with MET 270 (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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250B ILE* 3.9 28.3 - - - -
251B SER 4.0 11.0 - - - +
252B LEU* 3.9 15.8 - - + +
267B VAL* 3.8 14.4 - - + -
269B SER* 1.3 80.3 - - - +
271B GLN* 1.3 67.6 + - - +
276B PRO* 3.5 2.6 - - - +
277B ILE* 2.9 37.0 + - + +
278B THR* 3.3 42.2 - - - +
279B SER* 3.3 11.4 - - - +
280B ALA* 4.7 4.7 - - - -
286B LEU* 5.1 2.7 - - + -
287B GLY 3.2 8.5 - - - +
288B ILE* 4.3 12.1 - - + -
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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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269B SER* 5.5 6.2 - - - +
270B MET* 1.3 81.7 - - - +
272B MET* 1.3 62.1 + - - +
274B HIS* 4.1 5.1 - - - +
275B MET* 3.2 28.3 + - - +
276B PRO* 3.7 18.1 - - + +
277B ILE* 4.1 2.4 - - - +
286B LEU* 3.6 2.4 - - - +
287B GLY* 2.9 33.8 + - - +
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Residues in contact with MET 272 (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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7B ASN* 5.6 0.4 - - - -
87B GLN* 5.9 0.2 - - - +
271B GLN* 1.3 75.6 - - - +
273B PHE* 1.3 112.1 + - + +
274B HIS 3.2 2.9 - - - +
275B MET* 2.9 21.1 + - - +
277B ILE* 3.7 39.9 - - + +
279B SER 5.0 2.0 - - - +
284B ASP* 3.7 32.8 - - + +
285B ARG 3.0 29.8 - - - +
286B LEU* 4.2 4.3 - - + +
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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