Contacts of the strand formed by residues 285 - 290 (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 ARG 285 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B ASN* 3.9 22.4 - - - +
9B ASN* 4.5 3.4 - - - +
53B PHE* 3.5 33.9 - - - +
54B SER 5.5 0.2 + - - -
55B CYS* 6.0 2.0 - - - +
87B GLN* 5.5 2.8 + - - +
89B THR* 4.0 22.9 - - + +
229B ASP* 2.7 35.9 + - - -
230B HIS* 4.4 5.7 + - - -
242B THR* 4.5 8.6 + - - -
243B GLY* 3.5 12.6 - - - +
244B THR* 3.8 18.2 + - + +
272B MET* 3.0 25.4 - - - +
273B PHE* 5.7 0.3 - - - -
283B GLY 3.8 0.4 + - - -
284B ASP* 1.3 72.1 - - - +
286B LEU* 1.3 65.6 + - - +
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Residues in contact with LEU 286 (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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226B MET* 4.5 10.3 - - + -
242B THR* 3.2 8.2 - - - -
243B GLY 3.1 30.2 + - - +
245B ILE* 3.6 16.4 - - + -
270B MET* 5.1 3.8 - - + -
271B GLN 3.6 15.3 - - - +
272B MET* 4.2 7.9 - - + -
277B ILE* 4.5 9.2 - - + -
280B ALA* 3.5 32.1 - - + -
284B ASP* 4.3 11.0 - - + -
285B ARG* 1.3 76.3 - - - +
287B GLY* 1.3 64.3 + - - +
288B ILE* 3.3 35.2 - - + -
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Residues in contact with GLY 287 (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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240B VAL* 4.7 5.2 - - - -
241B MET 3.3 9.0 - - - -
242B THR* 4.0 11.9 - - - -
270B MET* 3.2 6.2 - - - +
271B GLN* 2.9 37.1 + - - +
286B LEU* 1.3 76.5 - - - +
288B ILE* 1.3 63.9 + - - +
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Residues in contact with ILE 288 (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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224B PHE* 4.7 5.4 - - + -
226B MET* 3.9 23.1 - - + -
239B THR 3.8 0.9 - - - +
240B VAL* 3.3 6.2 - - - -
241B MET* 2.8 52.4 + - + +
250B ILE* 3.9 26.9 - - + -
256B VAL* 5.4 2.7 - - + -
267B VAL* 3.7 27.4 - - + -
269B SER 3.3 9.4 - - - +
270B MET* 4.3 5.8 - - + -
286B LEU* 3.3 22.9 - - + -
287B GLY* 1.3 72.9 - - - +
289B CYS* 1.3 66.6 + - - +
290B VAL* 4.3 7.0 - - + -
303B VAL* 6.0 0.9 - - + -
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Residues in contact with CYS 289 (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* 3.7 44.6 - - - +
238B GLY 4.5 0.9 - - - -
239B THR 3.5 9.2 - - - -
240B VAL* 4.1 17.3 - - + -
268B LYS* 2.9 32.2 + - + +
269B SER* 2.8 36.1 + - - +
288B ILE* 1.3 73.5 - - - +
290B VAL* 1.3 67.6 + - - +
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Residues in contact with VAL 290 (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 4.2 2.6 - - - +
238B GLY* 3.7 4.3 - - - -
239B THR 3.1 28.4 + - - +
241B MET* 4.3 18.8 - - + -
256B VAL* 5.2 2.7 - - + -
258B ILE* 5.4 0.7 - - + -
265B LYS* 3.9 21.8 - - + +
266B LYS 3.1 26.2 - - - +
267B VAL* 3.9 11.4 - - + -
268B LYS* 4.4 5.2 - - - -
288B ILE* 4.3 9.2 - - + -
289B CYS* 1.3 82.2 - - - +
291B THR* 1.3 69.2 + - - +
292B GLN 3.1 3.5 + - - -
293B PHE* 4.2 19.5 - - + -
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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