Contacts of the helix formed by residues 391 - 402 (chain B) in PDB entry 6CP3
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 SER 391 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ALA* 3.1 1.0 - - - +
390B GLY* 1.3 77.9 - - - +
392B LEU* 1.3 53.9 + - - +
393B LYS 3.4 2.0 - - - -
394B LEU* 3.1 9.7 + - - +
395B PHE* 2.5 40.7 + - - +
451B VAL* 4.8 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ALA* 3.8 29.6 - - + -
158B LEU* 4.1 12.3 - - + -
389B ALA* 3.2 23.5 + - + +
391B SER* 1.3 75.5 - - - +
393B LYS* 1.3 61.5 + - - +
395B PHE* 4.2 4.5 - - + -
396B LEU* 2.9 39.2 + - + +
426B LEU* 3.7 36.8 - - + -
430B LEU* 5.4 7.9 - - + -
447B ILE* 4.1 19.7 - - + -
451B VAL* 4.6 15.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LEU* 3.7 42.6 + - + +
159B VAL* 4.9 0.2 - - - +
369B VAL* 4.6 11.5 + - + +
372B SER 3.8 20.4 + - - -
373B VAL* 4.2 19.3 - - + +
374B SER 6.1 0.2 - - - +
389B ALA 4.1 5.0 + - - +
390B GLY 5.1 1.8 - - - +
391B SER 3.4 0.2 - - - -
392B LEU* 1.3 79.2 - - - +
394B LEU* 1.3 64.2 + - + +
396B LEU* 3.3 4.5 + - - +
397B ALA* 2.9 28.5 + - + +
424F PHE* 4.6 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B GLY 4.4 13.7 + - - +
391B SER* 3.1 10.3 + - - +
393B LYS* 1.3 85.1 - - + +
395B PHE* 1.3 58.0 + - - +
397B ALA* 3.4 10.7 + - + +
398B GLN* 2.9 27.4 + - - +
424F PHE 5.1 4.9 - - - +
425F THR* 3.9 30.7 - - + +
426F GLY* 5.8 0.4 - - - -
458F TYR* 6.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B SER* 2.5 27.4 + - - +
392B LEU* 3.8 6.5 - - + +
393B LYS 3.2 0.2 - - - -
394B LEU* 1.3 74.5 - - - +
396B LEU* 1.3 61.5 + - + +
398B GLN* 3.2 11.0 + - + +
399B TYR* 2.9 25.9 + - + +
419B THR* 3.9 32.8 - - + -
422B ARG* 3.5 47.3 - - + -
423B GLY* 3.9 14.4 - - - -
426B LEU* 3.6 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LEU* 4.0 13.7 - - + -
369B VAL* 3.7 45.9 - - + +
392B LEU* 2.9 30.5 + - + +
393B LYS 4.0 1.3 - - - +
395B PHE* 1.3 75.7 - - + +
397B ALA* 1.3 60.8 + - - +
399B TYR* 3.8 22.5 - - + +
400B ARG* 2.9 29.6 + - - +
423B GLY* 4.9 2.0 - - - +
426B LEU* 4.6 21.8 - - + -
427B THR* 4.7 9.0 - - - +
430B LEU* 4.5 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B VAL* 5.6 0.6 - - - +
370B GLY* 6.3 2.2 - - - -
393B LYS* 2.9 15.1 + - + +
394B LEU* 3.5 17.3 - - + +
396B LEU* 1.3 77.4 - - - +
398B GLN* 1.3 56.2 + - - +
400B ARG* 3.2 21.8 + - - +
401B GLU* 2.9 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LEU 2.9 14.5 + - - +
395B PHE* 3.2 18.6 + - + +
397B ALA* 1.3 77.0 - - - +
399B TYR* 1.3 60.4 - - - +
401B GLU* 3.2 30.4 + - - +
402B VAL* 3.5 16.8 + - + +
419B THR* 4.8 21.5 - - + -
455F HIS* 3.8 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 2.9 18.7 + - + +
396B LEU* 3.8 15.9 - - + +
397B ALA 3.3 0.4 - - - -
398B GLN* 1.3 77.6 - - - +
400B ARG* 1.3 64.5 + - + +
402B VAL* 3.3 12.7 - - + +
403B ALA* 3.3 23.7 + - + +
419B THR* 3.9 13.7 - - - +
420B LEU* 3.6 40.7 - - + +
423B GLY* 3.5 28.5 - - - -
424B GLU* 3.4 20.8 + - - +
427B THR* 3.9 21.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ASN* 5.3 5.3 + - - +
370B GLY* 3.4 42.8 + - - +
371B LEU* 5.5 3.8 - - - +
396B LEU 2.9 18.1 + - - +
397B ALA* 3.2 17.2 + - - +
399B TYR* 1.3 78.5 - - + +
401B GLU* 1.3 75.2 + - - +
403B ALA* 3.3 22.0 + - + +
404B ALA 4.7 0.7 + - - -
341F GLU* 3.5 23.5 + - - +
342F LEU* 5.1 8.8 - - - +
343F GLY* 5.1 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B ALA* 2.9 23.7 + - - +
398B GLN* 3.2 22.4 + - - +
400B ARG* 1.3 89.2 + - - +
402B VAL* 1.3 60.8 + - + +
403B ALA 3.2 2.5 + - - -
404B ALA* 4.5 3.6 + - - +
405B PHE* 4.4 7.8 + - - +
342F LEU 4.0 16.5 - - - +
343F GLY* 5.8 0.2 - - - -
412F ARG* 4.0 20.9 + - - -
455F HIS* 5.3 13.5 - - + +
458F TYR* 6.0 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B GLN* 3.6 20.6 - - + +
399B TYR* 3.3 25.4 - - + +
401B GLU* 1.3 81.7 - - + +
403B ALA* 1.3 64.9 + - - +
404B ALA 3.5 0.7 - - - -
405B PHE* 3.8 20.4 - - + -
406B ALA* 3.4 22.5 + - + +
412B LEU* 6.5 0.9 - - + -
416B THR* 4.7 24.0 - - + +
419B THR* 4.8 12.6 - - - +
420B LEU* 4.9 11.7 - - + +
----------------------------------------------------------
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