Contacts of the strand formed by residues 354 - 358 (chain B) in PDB entry 1M2V
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 ILE 354 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 4.1 18.8 - - + -
349B CYS 3.8 2.2 - - - -
350B VAL* 4.4 12.6 - - + -
353B ALA* 1.3 76.4 - - - +
355B HIS* 1.3 62.4 + - - +
356B TYR* 3.4 30.0 - - + +
376B MET 3.5 1.9 - - - +
377B ASP* 3.9 0.5 - - - -
378B ILE* 2.9 41.1 + - + +
380B ASP 5.9 0.4 - - - +
381B LEU* 4.2 12.1 - - + -
423B ALA* 5.0 2.7 - - + +
426B PRO* 3.7 11.0 - - + -
427B ALA* 3.6 26.5 - - + +
430B SER* 3.1 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ARG* 3.9 7.4 - - - -
348B LEU* 3.5 7.2 - - - +
349B CYS* 2.8 52.1 + - + +
351B ASP* 3.0 30.7 + - - -
352B ASN* 5.5 0.4 - - - -
353B ALA* 3.2 15.8 + - + +
354B ILE* 1.3 72.9 - - - +
356B TYR* 1.3 63.3 + - - +
357B PHE* 3.3 8.6 - - + -
375B MET* 3.6 20.9 - - + -
376B MET 3.6 4.0 - - - -
377B ASP* 2.6 28.8 + - - +
414B PHE* 3.4 32.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B ILE 4.3 0.2 - - - -
348B LEU* 3.8 19.3 - - + -
354B ILE* 3.4 29.7 - - + +
355B HIS* 1.3 74.4 - - - +
357B PHE* 1.3 77.2 + - - +
375B MET* 3.4 1.4 - - - +
376B MET* 3.0 38.1 + - + +
378B ILE* 3.9 11.6 - - + +
385B PHE 3.7 12.5 + - - -
386B LEU* 3.4 24.4 - - + +
387B PRO* 3.5 33.9 - - + -
392B MET* 3.6 23.3 - - + -
430B SER* 2.9 30.3 + - - -
434B LEU* 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ILE* 4.6 1.8 - - + -
347B ILE* 3.2 34.7 + - + +
349B CYS* 3.7 30.3 - - + -
355B HIS* 3.3 17.0 - - + -
356B TYR* 1.3 81.4 - - - +
358B LYS* 1.3 63.6 + - - +
359B ILE* 3.3 10.5 + - + +
373B ILE* 5.2 0.2 - - + -
374B ASN 3.3 13.9 - - - +
375B MET* 3.2 44.6 - - + -
376B MET* 3.9 2.0 - - - -
391B SER 3.4 5.2 - - - +
392B MET* 3.8 14.0 - - - +
406B LEU* 3.4 46.2 - - + -
410B ILE* 4.6 3.4 - - + -
413B ILE* 4.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A SER* 5.9 0.8 + - - -
357B PHE* 1.3 71.2 - - - +
359B ILE* 1.3 62.8 + - - +
360B PRO* 3.7 16.7 - - - +
372B GLN 3.9 20.6 - - - +
373B ILE* 3.5 10.6 - - - +
374B ASN* 3.1 49.3 + - - +
376B MET* 3.2 22.8 - - + +
388B ARG* 3.9 30.0 - - - +
391B SER* 3.0 27.4 - - - -
392B MET* 4.6 0.4 - - - -
----------------------------------------------------------
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