Contacts of the strand formed by residues 355 - 365 (chain B) in PDB entry 4Y5U
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 CYS 355 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B GLN* 4.5 2.7 - - - +
294B ARG* 3.1 32.8 - - - +
299B LEU* 3.5 14.0 - - - +
348B GLU 3.8 0.5 - - - +
349B ASN* 3.6 0.5 - - - -
350B SER* 3.1 33.4 + - - -
353B GLY* 3.6 21.8 - - - +
354B ASN* 1.3 76.4 - - - +
356B CYS* 1.3 61.7 + - - +
357B SER* 3.9 18.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B GLN* 5.1 0.6 + - - -
294B ARG* 3.2 6.7 - - - +
295B PHE* 2.7 49.6 + - - +
298B GLY* 3.7 21.3 - - - -
299B LEU* 4.4 0.4 - - - +
302B LEU* 4.4 5.4 - - - -
347B LEU* 3.7 32.8 - - - -
348B GLU 3.5 9.4 - - - -
349B ASN* 3.3 22.4 - - - +
355B CYS* 1.3 75.2 - - - +
357B SER* 1.3 56.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLU* 5.1 4.5 - - - -
292B GLY* 6.5 0.2 - - - -
293B VAL 3.3 12.3 - - - -
294B ARG* 4.2 8.7 - - - -
346B PRO 4.0 0.9 - - - +
347B LEU* 3.7 6.7 - - - -
348B GLU* 3.0 30.2 + - - +
355B CYS* 3.9 18.0 - - - -
356B CYS* 1.3 76.5 - - - +
358B ALA* 1.3 63.4 + - - +
359B LEU* 4.1 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B GLY* 3.5 1.4 - - - -
293B VAL* 2.9 41.8 + - + +
311B VAL* 4.2 9.2 - - + -
345B VAL* 3.4 24.7 - - + -
346B PRO 3.6 9.4 - - - +
347B LEU* 3.6 16.5 - - + +
357B SER* 1.3 73.9 - - - +
359B LEU* 1.3 61.7 + - - +
360B PHE* 3.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LYS* 4.6 11.9 - - + -
290B GLN* 4.0 20.0 - - - +
291B ALA 3.7 19.3 - - - +
292B GLY* 4.2 4.0 - - - -
345B VAL* 3.7 16.6 - - - +
357B SER* 4.1 5.0 + - - -
358B ALA* 1.3 74.8 - - - +
360B PHE* 1.3 64.3 + - - +
361B LYS* 3.1 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PHE 3.8 1.0 - - - +
290B GLN* 3.3 26.3 - - - +
291B ALA 2.9 19.9 + - - +
293B VAL* 3.8 13.2 - - + -
311B VAL* 3.6 42.4 - - + -
313B ALA* 4.1 7.0 - - + -
342B ASN 4.2 5.6 - - - +
343B ASN 3.8 11.4 - - - -
345B VAL* 3.7 26.9 - - + -
358B ALA 3.6 17.9 - - - -
359B LEU* 1.3 71.5 - - - +
361B LYS* 1.3 64.0 + - - +
362B ASN 3.4 1.8 - - - +
363B LEU* 3.4 37.9 - - + -
388B PHE* 4.0 19.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LYS* 3.1 17.8 + - - +
289B PHE 3.8 2.3 - - - +
290B GLN* 3.4 31.3 + - - +
359B LEU* 3.1 43.2 + - + +
360B PHE* 1.3 71.4 - - - +
362B ASN* 1.3 73.2 + - - +
363B LEU 3.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LYS* 2.5 38.2 + - + +
341B ILE* 4.1 1.6 - - - +
342B ASN* 3.5 38.3 - - - +
360B PHE* 3.4 1.6 - - - +
361B LYS* 1.3 88.7 - - - +
363B LEU* 1.3 64.9 + - - +
364B LEU* 3.6 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LYS* 3.3 4.9 - - - -
289B PHE* 2.5 71.4 + - + +
291B ALA* 4.0 22.9 - - + +
313B ALA* 4.8 8.5 - - + -
340B ILE* 4.0 10.8 - - + -
341B ILE 3.7 4.5 - - - +
342B ASN 3.1 29.4 - - - +
343B ASN* 4.3 4.3 - - - -
360B PHE* 3.4 39.9 - - + -
362B ASN* 1.3 77.5 - - - +
364B LEU* 1.3 55.3 + - - +
386B VAL* 6.0 1.8 - - + -
388B PHE* 5.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B GLN* 4.0 13.9 - - + +
287B THR* 3.7 31.9 - - - +
288B LYS* 4.0 9.0 - - + +
289B PHE* 3.7 4.5 - - - -
340B ILE* 2.9 16.8 - - - +
341B ILE* 2.9 41.2 + - + -
362B ASN 4.4 2.5 - - - +
363B LEU* 1.3 76.8 - - - +
365B LEU* 1.3 75.3 + - - +
366B LYS* 3.5 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B LEU* 4.4 8.5 - - + -
284B LYS 5.3 1.6 - - - +
285B THR* 3.8 15.8 - - + -
286B GLN* 2.8 31.2 + - - +
287B THR 4.1 2.6 + - - -
289B PHE* 3.7 17.5 - - + -
315B MET* 3.8 26.0 - - + -
339B GLU* 3.6 29.8 - - + -
340B ILE* 4.0 10.8 - - + -
364B LEU* 1.3 77.5 - - - +
366B LYS* 1.3 68.5 + - - +
412B VAL* 4.0 36.8 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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