Contacts of the helix formed by residues 635 - 649 (chain B) in PDB entry 2PZI
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 HIS 635 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A VAL* 3.9 16.2 - - + +
481A ASP* 3.5 14.4 + - - -
755A GOL 3.1 27.3 + - - -
421B THR* 3.4 17.3 + - + +
424B VAL* 3.8 24.4 - - + +
603B ILE* 4.0 28.7 - - + -
607B PHE* 4.2 1.5 - - + -
629B VAL* 4.4 3.1 - - + -
633B SER* 2.9 19.3 + - - +
634B ARG* 1.3 81.0 + - + +
636B PHE* 1.3 63.0 + - - +
637B THR 3.3 3.5 + - - -
638B THR* 3.4 9.2 + - - -
639B ALA* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 636 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B VAL* 3.4 31.0 - - + -
630B PRO 3.5 9.2 - - - +
631B PRO* 3.7 33.7 - - + +
633B SER* 3.2 18.4 + - - +
634B ARG 3.4 1.0 - - - -
635B HIS* 1.3 77.6 - - - +
637B THR* 1.3 64.2 + - - +
639B ALA* 3.4 2.4 + - + +
640B ARG* 3.0 77.1 + - + +
671B LEU* 4.6 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 637 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B ARG 4.8 3.9 + - - -
635B HIS 3.3 0.6 - - - -
636B PHE* 1.3 82.3 - - - +
638B THR* 1.3 57.8 + - - +
640B ARG* 3.0 6.7 + - - +
641B LEU* 2.8 52.6 + - + +
671B LEU* 4.3 9.4 - - + +
672B PRO* 4.4 18.3 - - + +
675B GLU* 5.0 9.2 - - + -
678B VAL* 4.3 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 638 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B VAL* 3.4 41.0 - - + +
425B ASP* 4.3 2.9 - - + -
428B VAL* 3.7 23.6 - - + -
607B PHE* 4.1 0.7 - - + -
634B ARG 4.9 2.1 + - - -
635B HIS* 3.4 14.9 + - - -
637B THR* 1.3 79.0 - - - +
639B ALA* 1.3 53.7 + - - +
641B LEU* 3.4 10.4 + - - +
642B THR* 2.5 39.3 + - - +
677B ARG* 4.8 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 639 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B PHE* 3.5 23.0 - - + -
626B LEU* 3.9 16.5 - - + +
629B VAL* 3.9 26.5 - - + -
635B HIS 3.0 13.5 + - - +
636B PHE* 3.5 9.9 - - + +
637B THR 3.2 0.2 - - - -
638B THR* 1.3 77.8 - - - +
640B ARG* 1.3 58.2 + - + +
642B THR* 3.4 2.3 + - - -
643B SER* 3.0 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 640 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626B LEU 4.7 3.0 + - - -
627B ASP* 3.0 60.1 + - - +
636B PHE* 3.0 60.2 + - + +
637B THR 3.0 5.6 + - - +
639B ALA* 1.3 76.0 - - + +
641B LEU* 1.3 62.6 + - - +
643B SER* 3.1 19.5 - - - -
644B ALA* 3.3 8.0 + - - +
667B ARG* 4.5 21.0 - - + +
671B LEU* 3.8 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 641 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B VAL* 3.8 16.8 - - + -
637B THR* 2.8 38.2 + - + +
638B THR* 3.8 8.3 - - - +
640B ARG* 1.3 71.6 - - - +
642B THR* 1.3 58.7 + - - +
644B ALA* 3.2 6.9 + - - +
645B VAL* 3.0 29.8 + - - +
668B VAL* 4.5 10.1 - - + -
671B LEU* 3.7 20.2 - - + -
677B ARG* 3.9 34.8 - - + +
678B VAL* 4.0 14.1 - - - +
681B ILE* 3.8 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 642 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B VAL 4.4 1.7 + - - -
427B LEU* 3.5 31.7 + - + +
428B VAL* 3.8 15.3 + - - +
607B PHE* 3.5 27.1 - - + -
610B ALA* 6.1 0.9 - - + -
626B LEU* 4.0 11.7 - - + -
638B THR* 2.5 31.2 + - - +
639B ALA 3.7 4.7 - - - -
641B LEU* 1.3 69.5 - - - +
643B SER* 1.3 55.7 + - - +
645B VAL* 3.7 3.3 - - - +
646B THR* 2.6 46.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 643 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623B VAL* 3.9 10.1 + - - +
626B LEU* 3.4 25.9 - - - +
627B ASP* 3.7 13.3 + - - -
639B ALA 3.0 15.0 + - - -
640B ARG* 3.1 14.4 - - - -
642B THR* 1.3 76.5 - - - +
644B ALA* 1.3 62.8 + - - -
646B THR* 3.2 5.2 + - - -
647B LEU* 3.0 28.4 + - - +
667B ARG* 3.7 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 644 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B ARG 3.3 7.2 + - - +
641B LEU 3.2 10.1 + - - +
643B SER* 1.3 79.3 - - - +
645B VAL* 1.3 62.3 + - - +
647B LEU* 3.1 16.4 + - - +
648B LEU* 3.4 11.5 + - - +
664B ALA* 3.8 29.8 - - + +
667B ARG* 4.3 3.9 - - + +
668B VAL* 3.7 30.1 - - + -
681B ILE* 4.4 5.4 - - + -
685B VAL* 4.6 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 645 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LEU* 3.8 41.5 - - + +
428B VAL* 4.6 1.8 - - + -
641B LEU 3.0 19.1 + - - +
642B THR* 3.8 7.9 - - - +
644B ALA* 1.3 75.0 - - - +
646B THR* 1.3 56.7 + - - +
648B LEU* 2.9 25.7 + - + +
649B SER* 2.9 27.0 + - - +
681B ILE* 3.9 27.4 - - + -
684B LEU* 4.0 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 646 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LEU* 3.7 16.6 - - - +
610B ALA* 5.7 0.7 - - + +
614B SER* 3.3 23.7 + - - +
619B ARG* 3.4 21.3 + - + +
622B ALA* 4.0 19.9 - - + +
623B VAL* 4.4 11.0 - - + +
626B LEU* 4.1 5.1 - - - +
642B THR* 2.6 32.8 + - - +
643B SER* 3.3 8.7 - - - +
645B VAL* 1.3 73.8 - - - +
647B LEU* 1.3 60.8 + - - +
648B LEU 3.1 0.9 + - - -
649B SER* 3.2 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 647 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B ARG* 4.2 13.3 - - + +
620B VAL* 6.1 1.3 - - + -
623B VAL* 3.9 19.3 - - + -
643B SER 3.0 19.8 + - - +
644B ALA 3.1 7.1 + - - +
646B THR* 1.3 75.0 - - - +
648B LEU* 1.3 59.0 + - - +
649B SER 3.5 0.2 - - - -
656B VAL* 3.4 28.8 - - - +
660B GLN* 3.8 43.3 - - + +
663B ASP* 3.9 11.9 - - - +
664B ALA* 3.8 19.3 - - + +
667B ARG* 3.7 32.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 648 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B ALA 3.8 11.7 - - - +
645B VAL* 2.9 11.7 + - + +
647B LEU* 1.3 80.4 - - - +
649B SER* 1.3 58.7 + - - +
656B VAL* 4.4 9.3 - - + +
661B ILE* 3.6 41.5 - - + -
664B ALA* 4.4 4.3 - - + -
684B LEU* 4.1 12.8 - - + +
685B VAL* 3.7 45.3 - - + +
688B GLY* 4.9 7.0 - - - -
689B ALA 4.8 6.5 - - - +
692B TRP* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 649 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LEU* 4.4 8.7 - - - +
614B SER* 5.4 6.3 - - - -
619B ARG* 3.4 35.1 + - - -
645B VAL* 2.9 28.4 + - - +
646B THR* 3.2 12.4 + - - -
648B LEU* 1.3 81.8 - - - +
656B VAL* 4.8 0.9 - - - -
----------------------------------------------------------
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