Contacts of the strand formed by residues 368 - 376 (chain B) in PDB entry 3D8F
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 LYS 368 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TRP 3.8 3.4 - - - -
378A VAL* 3.7 26.2 - - + -
400A GLN* 3.2 22.5 + - - +
366B GLY* 3.3 22.2 + - - +
367B ILE* 1.3 78.1 - - - +
369B CYS* 1.3 64.2 + - - +
370B PHE* 3.5 23.6 - - + -
424B LEU 4.0 0.4 - - - +
425B GLN* 3.4 2.4 - - - -
426B LEU* 3.1 34.2 + - + -
494B SER* 2.9 35.6 + - - +
497B GLU* 4.5 11.3 + - - -
498B ILE* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LEU 3.9 0.3 - - - +
376A GLY* 3.1 24.6 - - - -
377A TRP* 2.8 56.5 + - + +
378A VAL* 5.1 0.4 - - - +
401A LEU* 4.1 3.5 - - - +
368B LYS* 1.3 77.3 - - - +
370B PHE* 1.3 58.9 + - - +
423B LEU* 3.8 31.4 - - - -
424B LEU 3.7 3.4 - - - -
425B GLN* 3.4 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LEU 4.1 2.7 - - - -
400A GLN* 3.6 19.1 - - - -
401A LEU* 3.4 27.1 - - + -
368B LYS* 3.5 29.6 - - + -
369B CYS* 1.3 71.6 - - - +
371B ALA* 1.3 64.1 + - - +
372B VAL* 3.5 5.5 + - + +
423B LEU* 4.6 1.8 - - - -
424B LEU* 2.9 53.0 + - + +
426B LEU* 4.0 15.3 - - + -
484B CYS* 5.9 0.4 - - + -
486B ALA* 4.2 15.7 - - + -
490B ASN* 4.0 12.1 - - + -
491B ILE* 3.6 39.0 - - + -
494B SER* 3.9 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A SER 3.7 13.5 - - - +
375A LEU* 3.0 32.4 + - - +
369B CYS 3.8 1.0 + - - -
370B PHE* 1.3 72.3 - - - +
372B VAL* 1.3 64.5 + - - +
422B LEU 4.1 4.5 - - - -
423B LEU* 4.1 15.7 - - + +
484B CYS* 4.4 0.3 - - - +
485B GLU* 3.2 33.2 + - + +
486B ALA* 5.0 0.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B PHE* 3.6 14.6 - - + +
371B ALA* 1.3 79.7 - - - +
373B ARG* 1.3 58.1 + - - +
421B ASP* 3.7 4.5 - - - +
422B LEU* 2.8 49.6 + - + +
424B LEU* 4.0 20.9 - - + -
482B PHE* 3.8 32.8 - - + -
483B ARG 3.1 9.6 - - - +
484B CYS* 3.5 27.6 - - + -
485B GLU* 5.0 1.3 - - - +
491B ILE* 4.5 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A LYS 6.0 0.4 - - - +
372B VAL* 1.3 72.2 - - - +
374B SER* 1.3 74.8 + - - +
375B LEU* 3.4 12.1 + - - +
419B GLY* 3.9 24.6 + - - -
420B LYS 3.4 7.9 - - - +
421B ASP* 3.0 39.6 + - - +
482B PHE* 3.4 1.6 - - - -
483B ARG* 2.7 53.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B VAL 4.0 1.2 + - - -
373B ARG* 1.3 77.9 - - - +
375B LEU* 1.3 60.9 + - - +
376B GLY* 3.5 8.5 + - - -
416B TRP* 3.4 19.8 + - - -
417B GLY* 3.0 23.9 + - - -
419B GLY* 3.0 24.4 + - - -
420B LYS 2.6 15.2 + - - -
422B LEU* 4.6 5.9 - - - +
480B HIS* 6.2 0.2 - - - +
481B VAL 3.9 3.8 + - - -
482B PHE* 3.8 25.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ARG* 3.4 10.9 + - - +
374B SER* 1.3 77.2 - - - +
376B GLY* 1.3 59.2 + - - +
398B ILE* 5.7 0.2 - - + -
401B LEU* 3.6 36.8 - - + +
402B SER* 4.7 0.9 - - - +
418B GLU* 2.9 27.6 - - + +
419B GLY 4.7 0.9 - - - +
464B ASP* 4.8 2.0 - - - +
481B VAL* 2.9 41.0 + - + +
482B PHE 4.4 0.9 - - - +
483B ARG* 3.7 52.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B SER* 3.5 9.6 + - - -
375B LEU* 1.3 80.2 - - - +
377B TRP* 1.3 64.6 + - - -
401B LEU* 3.4 16.1 - - - +
417B GLY* 4.9 0.9 - - - -
418B GLU* 3.9 22.6 - - - +
480B HIS* 4.8 1.8 - - - -
481B VAL 3.3 20.5 + - - -
----------------------------------------------------------
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