Contacts of the helix formed by residues 657 - 670 (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 THR 657 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655B GLU 5.5 1.8 - - - +
656B VAL* 1.3 87.0 - - - +
658B GLU* 1.3 64.0 + - - +
659B GLU* 3.6 8.6 + - - +
660B GLN* 2.8 54.0 + - - +
661B ILE* 3.4 6.9 - - - +
692B TRP* 3.9 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 658 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657B THR* 1.3 73.2 - - - +
659B GLU* 1.3 65.5 + - - +
661B ILE* 3.2 16.0 + - - +
662B ARG* 2.5 48.8 + - - +
692B TRP* 3.5 26.8 - - + -
697B LYS 4.2 3.6 - - - +
698B ALA* 3.5 12.8 - - + +
699B SER* 2.8 35.2 + - - -
708B PHE* 4.5 2.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 659 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657B THR* 3.2 9.6 + - - +
658B GLU* 1.3 80.8 - - + +
660B GLN* 1.3 57.5 - - + +
662B ARG* 3.6 17.5 + - - -
663B ASP* 3.2 24.6 + - - +
666B ARG* 3.6 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 660 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B ARG* 4.5 22.0 + - - +
620B VAL* 4.9 12.7 - - - +
647B LEU* 3.8 32.7 - - + +
655B GLU 4.8 1.2 - - - +
656B VAL* 3.6 18.2 - - + +
657B THR* 2.8 51.6 + - - +
658B GLU 3.2 0.6 - - - -
659B GLU* 1.3 76.9 - - + +
661B ILE* 1.3 60.6 + - - +
663B ASP* 3.5 7.2 + - - +
664B ALA* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 661 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B LEU* 3.6 27.1 - - + -
656B VAL* 3.9 7.2 - - + -
657B THR 3.4 18.4 + - - +
658B GLU* 3.2 7.0 + - - +
660B GLN* 1.3 75.0 - - - +
662B ARG* 1.3 58.2 + - - +
664B ALA* 3.3 7.2 - - - +
665B ALA* 2.9 26.5 + - - +
685B VAL* 4.2 6.0 - - + +
689B ALA* 4.0 17.0 - - + -
692B TRP* 3.5 49.1 - - + +
703B ILE* 4.0 7.6 - - + -
708B PHE* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 662 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658B GLU* 2.5 54.9 + - - +
659B GLU* 3.9 20.2 - - - +
660B GLN 3.4 0.2 - - - -
661B ILE* 1.3 72.6 - - - +
663B ASP* 1.3 54.8 + - - +
665B ALA* 3.6 1.6 - - - +
666B ARG* 2.8 56.2 + - - +
699B SER* 3.3 10.5 + - - -
701B ASN* 2.3 52.8 + - - +
702B HIS 4.3 4.6 + - - -
703B ILE* 4.1 20.6 - - + +
708B PHE* 3.4 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 663 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623B VAL* 5.3 1.4 - - - +
647B LEU* 3.9 12.3 - - + +
659B GLU* 3.2 18.3 + - - +
660B GLN* 3.6 8.1 - - - +
661B ILE 3.3 0.2 - - - -
662B ARG* 1.3 73.2 - - - +
664B ALA* 1.3 57.4 + - - +
666B ARG* 3.5 23.5 + - - +
667B ARG* 2.8 66.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 664 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B ALA* 3.8 29.5 - - + +
647B LEU* 3.8 14.2 - - + +
648B LEU* 4.4 6.3 - - + -
660B GLN 3.0 15.3 + - - +
661B ILE* 3.3 12.8 - - - +
663B ASP* 1.3 77.8 - - - +
665B ALA* 1.3 62.9 + - - +
667B ARG* 3.2 5.2 - - - +
668B VAL* 3.1 23.9 + - - +
685B VAL* 4.4 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 665 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661B ILE 2.9 16.5 + - - +
662B ARG 3.6 4.7 - - - +
664B ALA* 1.3 75.3 - - - +
666B ARG* 1.3 59.0 + - - +
668B VAL* 3.0 4.0 + - - -
669B GLU* 2.9 30.2 + - - +
685B VAL* 4.1 12.1 - - + +
703B ILE* 3.7 24.9 - - + -
704B LEU* 3.4 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 666 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659B GLU* 3.6 24.4 + - - -
662B ARG* 2.8 38.1 + - - +
663B ASP* 3.5 33.1 + - - +
665B ALA* 1.3 71.2 - - - +
667B ARG* 1.3 62.3 + - - +
669B GLU* 3.5 20.3 + - - +
670B ALA* 3.4 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 667 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623B VAL* 3.3 18.8 - - - +
627B ASP* 3.0 40.6 + - - -
640B ARG* 4.5 23.0 - - + +
643B SER* 3.7 20.1 - - - -
644B ALA* 4.3 8.1 - - + +
647B LEU* 3.7 18.4 - - - +
663B ASP* 2.8 47.0 + - - +
664B ALA* 3.2 9.6 + - - +
666B ARG* 1.3 74.4 - - - +
668B VAL* 1.3 60.7 + - - +
670B ALA* 3.5 10.7 + - - +
671B LEU* 3.5 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 668 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B LEU* 4.5 9.0 - - + -
644B ALA* 3.7 20.4 - - + -
664B ALA 3.3 13.7 - - - +
665B ALA* 3.0 6.9 + - - +
667B ARG* 1.3 73.3 - - - +
669B GLU* 1.3 64.9 + - - +
670B ALA 2.9 5.4 + - - -
671B LEU* 3.0 22.7 + - + +
678B VAL* 3.7 21.4 - - + +
681B ILE* 4.0 14.1 - - + -
682B ARG* 3.4 35.8 - - + +
685B VAL* 4.2 9.2 - - + -
704B LEU* 4.4 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 669 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665B ALA* 2.9 17.2 + - - +
666B ARG* 3.5 23.6 + - - +
668B VAL* 1.3 74.6 - - - +
670B ALA* 1.3 60.1 + - - +
671B LEU 3.4 6.6 + - - +
682B ARG* 4.6 10.5 - - - +
702B HIS 5.3 1.0 - - - +
703B ILE* 4.9 1.4 - - - -
704B LEU* 3.4 42.7 + - + +
705B GLY 4.9 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 670 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666B ARG 3.4 14.5 + - - +
667B ARG* 3.7 9.2 - - - +
668B VAL 2.9 1.2 + - - -
669B GLU* 1.3 78.8 - - + +
671B LEU* 1.3 65.6 + - + +
672B PRO* 4.7 0.7 - - - +
----------------------------------------------------------
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