Contacts of the strand formed by residues 371 - 377 (chain B) in PDB entry 3SV1
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 371 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ARG 3.4 5.6 - - - -
410A LYS* 3.8 24.9 - - + -
411A ALA* 3.9 7.9 - - + +
414A ILE* 4.0 20.0 - - + -
366B ASP* 4.5 13.5 - - + -
367B LEU* 3.7 22.4 - - + +
370B GLY* 1.3 76.9 - - - -
372B ILE* 1.3 74.7 + - - +
373B PHE* 3.3 31.6 - - + -
433B PHE* 3.4 2.9 - - - -
434B ILE* 3.3 36.5 + - + +
516B SER* 3.8 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ARG* 3.7 27.4 - - - +
407A ARG* 3.2 38.3 + - + +
408A MET* 3.7 18.5 - - + +
411A ALA* 3.3 14.3 - - - +
371B ILE* 1.3 89.7 - - - +
373B PHE* 1.3 72.0 + - - +
431B ASP* 3.6 20.9 - - + +
432B LEU 3.2 18.4 - - - +
433B PHE* 4.1 15.3 - - + -
442B LEU* 6.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A ALA* 3.8 29.8 - - + -
414A ILE* 4.7 11.2 - - + -
415A LYS* 5.2 6.5 - - + -
371B ILE* 3.3 31.2 - - + -
372B ILE* 1.3 80.3 - - - +
374B ALA* 1.3 61.2 + - - +
431B ASP* 3.8 0.3 - - - -
432B LEU* 3.0 30.5 + - + +
434B ILE* 3.8 18.2 - - + -
509B ASP* 3.4 27.4 - - + +
512B LEU* 4.3 16.4 - - + -
513B ILE* 3.9 27.8 - - + -
516B SER* 3.5 22.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B PHE* 1.3 77.6 - - - +
375B ALA* 1.3 61.1 + - - +
430B VAL 3.3 11.0 - - - +
431B ASP* 5.0 5.8 - - - +
444B ALA* 6.1 2.5 - - + -
507B SER* 3.0 20.1 + - - -
509B ASP* 4.7 5.6 + - - +
513B ILE* 4.5 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B PHE 4.3 0.2 - - - -
374B ALA* 1.3 76.7 - - - +
376B ASN* 1.3 69.9 + - - +
429B GLU* 3.7 1.0 - - - +
430B VAL* 2.9 31.8 + - + -
432B LEU* 3.8 25.5 - - + +
468B VAL* 6.0 0.2 - - + -
505B PHE* 4.0 16.4 - - + -
506B GLU 3.2 13.9 - - - +
507B SER* 3.7 9.4 - - - -
513B ILE* 4.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ALA* 1.3 79.2 + - - +
377B TYR* 1.3 63.5 + - - +
378B LEU* 3.2 4.0 + - + +
427B LEU* 3.1 35.6 - - + +
428B THR 3.5 3.4 + - - +
429B GLU* 3.9 25.1 - - - +
505B PHE* 3.1 8.1 - - - -
506B GLU* 2.6 51.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B ASN* 1.3 69.6 - - - +
378B LEU* 1.3 61.2 + - - +
379B GLY* 3.4 29.6 - - - -
380B SER* 2.4 29.7 + - - -
426B THR 4.8 0.2 - - - +
427B LEU* 3.6 2.9 - - - -
428B THR* 2.7 45.3 + - + +
430B VAL* 3.9 15.8 - - + +
450B MET* 4.2 16.4 - - + -
451B MET* 4.5 20.7 - - + +
503B HIS* 4.0 14.6 + - + -
504B VAL 3.4 11.7 - - - -
505B PHE* 3.5 27.6 - + + -
----------------------------------------------------------
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