Contacts of the helix formed by residues 654 - 671 (chain A) in PDB entry 4FYT
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 PRO 654 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A ILE* 3.7 22.9 - - + -
594A GLY* 5.7 2.5 - - - +
624A LEU* 3.7 24.0 - - + -
625A ASN* 3.9 14.6 - - - +
651A SER 5.4 0.4 - - - +
652A ALA 4.1 4.0 - - - +
653A ILE* 1.4 88.5 - - + +
655A VAL* 1.3 65.4 + - - +
657A ASN* 2.9 27.9 + - - +
658A ARG 3.0 9.7 + - - -
1D NAG 5.2 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 655 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ASP* 5.5 1.6 - - - +
653A ILE 3.4 1.8 + - - -
654A PRO* 1.3 70.7 - - - +
656A ILE* 1.3 74.6 + - + +
658A ARG* 3.1 30.9 + - - +
659A ALA* 3.2 10.4 + - - +
691A GLN* 3.8 24.5 - - + +
693A MET* 4.2 13.0 - - + -
694A PRO* 3.7 29.8 - - + +
1023A SO4 4.4 6.9 + - - +
1D NAG 4.9 8.7 - - - -
2D NAG 4.6 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 656 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ASP* 3.7 33.4 - - + +
436A VAL* 3.7 24.9 - - + +
485A ARG* 4.8 2.9 - - - +
625A ASN* 3.5 58.8 - - + +
626A VAL* 3.8 7.5 - - + +
654A PRO* 3.3 2.0 - - - +
655A VAL* 1.3 81.2 - - + +
657A ASN* 1.3 58.6 + - - +
659A ALA* 3.2 5.7 + - - +
660A GLN* 2.9 22.9 + - - +
693A MET* 3.7 26.7 - - + -
1D NAG 4.2 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 657 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A ILE* 5.3 2.2 - - - +
621A LEU* 4.3 11.7 - - + +
622A LEU 4.0 2.4 + - - -
623A ASN 2.9 28.5 + - - -
624A LEU* 3.6 15.2 - - - +
625A ASN* 2.9 23.2 + - - +
626A VAL* 4.4 1.2 - - - +
653A ILE* 3.9 15.0 - - + -
654A PRO* 2.9 19.4 + - + +
656A ILE* 1.3 75.9 - - - +
658A ARG* 1.3 59.5 + - - +
660A GLN* 2.9 27.0 + - - +
661A ILE* 2.9 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 658 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A LEU* 4.1 8.3 - - + -
650A HIS* 3.3 29.4 + - - -
651A SER* 3.9 3.2 + - - +
653A ILE* 2.8 39.5 + - + +
654A PRO 3.0 9.4 + - - +
655A VAL* 3.1 20.9 + - - +
657A ASN* 1.3 76.2 - - - +
659A ALA* 1.3 60.3 + - - +
661A ILE* 3.4 10.2 + - - +
662A ILE* 3.3 27.0 + - - +
685A PHE* 4.0 18.6 - - + -
689A GLU* 2.7 41.1 + - - -
691A GLN* 3.4 10.9 - - - +
694A PRO* 3.9 12.5 - - + +
1023A SO4 3.1 36.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 659 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A VAL* 5.4 1.3 - - + -
437A LEU* 4.8 4.0 - - + -
441A TYR* 4.6 4.7 - - + -
655A VAL 3.2 7.1 + - - +
656A ILE 3.3 9.2 - - - +
658A ARG* 1.3 75.1 - - - +
660A GLN* 1.3 58.1 + - - +
662A ILE* 3.3 3.7 + - - +
663A ASN* 2.8 33.1 + - - +
693A MET* 3.7 31.2 - - + +
694A PRO* 4.1 7.7 - - + +
697A ALA* 3.7 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 660 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A TYR* 3.4 28.4 + - - +
621A LEU* 4.8 3.5 - - - +
622A LEU 2.9 24.8 + - - +
623A ASN* 3.5 17.8 + - - +
626A VAL* 3.7 15.5 - - + +
630A TYR 5.5 0.2 + - - -
632A VAL* 3.9 9.6 - - - +
634A TYR* 4.7 7.3 + - - -
656A ILE 2.9 7.8 + - - +
657A ASN* 2.9 33.7 + - - +
658A ARG 3.3 0.2 - - - -
659A ALA* 1.3 74.4 - - - +
661A ILE* 1.3 66.8 + - - +
664A ASP* 2.7 54.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 661 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A LEU* 4.0 20.9 - - + -
634A TYR* 5.8 0.7 - - + -
639A TRP* 4.0 17.7 - - + -
642A ILE* 3.6 25.8 - - + -
646A LEU* 4.2 15.9 - - + -
653A ILE* 4.0 25.4 - - + -
657A ASN 2.9 23.7 + - - +
658A ARG* 3.4 8.3 + - - +
660A GLN* 1.3 78.3 - - - +
662A ILE* 1.3 64.6 + - + +
664A ASP* 5.0 0.7 - - - -
665A ALA* 3.2 26.0 + - - +
682A ASN* 3.3 28.6 + - + +
685A PHE* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 662 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A ARG 3.3 14.9 + - - +
659A ALA* 3.7 5.4 - - - +
660A GLN 3.2 0.6 - - - -
661A ILE* 1.3 79.0 - - + +
663A ASN* 1.3 66.8 + - - +
665A ALA* 4.0 1.2 - - - +
666A PHE* 3.2 48.0 + - + -
682A ASN* 3.8 26.2 - - + +
683A THR* 4.4 1.3 - - + -
685A PHE* 3.8 22.7 - - + -
686A LEU* 4.0 15.7 - - + -
694A PRO* 3.7 23.3 - - + +
697A ALA 4.3 1.3 - - - -
698A ALA* 3.6 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 663 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LEU* 5.9 0.8 - - - +
441A TYR* 3.5 36.7 + - + +
631A ARG* 2.8 37.1 + - - -
659A ALA 2.8 20.1 + - - +
662A ILE* 1.3 76.8 - - - +
664A ASP* 1.3 61.6 + - - +
666A PHE* 3.3 1.2 + - - +
667A ASN* 2.8 33.6 + - - +
697A ALA* 4.1 15.9 + - + +
700A SER* 4.9 5.7 - - - -
701A SER* 3.3 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 664 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A TYR* 3.6 8.0 + - - -
630A TYR 4.7 0.3 - - - +
631A ARG* 2.8 45.2 + - - +
632A VAL* 3.0 41.4 + - - +
639A TRP* 5.0 2.7 - - + -
660A GLN* 2.7 46.6 + - + +
661A ILE* 4.5 2.2 - - - +
663A ASN* 1.3 73.4 - - - +
665A ALA* 1.3 57.3 + - - +
667A ASN* 3.2 2.6 + - - +
668A LEU* 2.8 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 665 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A TRP* 4.2 9.4 - - + -
661A ILE 3.2 10.1 + - - +
662A ILE 4.0 1.8 - - - +
664A ASP* 1.3 78.6 - - - +
666A PHE* 1.3 58.2 + - - +
668A LEU* 3.4 10.8 + - - +
669A ALA* 2.9 29.5 + - - +
674A VAL* 3.5 6.3 - - + +
678A LEU* 4.2 8.1 - - + -
679A ALA* 3.5 16.1 - - - +
682A ASN* 3.2 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 666 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A ILE* 3.2 34.2 + - + +
663A ASN 3.8 0.7 - - - +
665A ALA* 1.3 74.9 - - - +
667A ASN* 1.3 63.1 + - - +
669A ALA* 3.3 4.4 + - + +
670A SER* 3.2 23.2 + - - -
676A VAL* 5.5 0.7 - - + -
679A ALA* 3.7 26.7 - - + +
680A LEU* 3.9 15.5 - - + -
683A THR* 3.5 33.0 - - + -
698A ALA 5.0 0.7 - - - -
701A SER* 3.4 34.3 - - - +
702A LEU* 3.8 19.7 - - + -
705A PHE* 3.6 41.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 667 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A MET 5.5 1.0 - - - +
445A ALA* 5.3 5.7 - - - +
448A ALA* 5.9 0.2 - - - +
566A PHE* 3.4 17.6 - - + -
568A LEU* 3.7 21.7 - - - +
631A ARG* 3.3 33.6 + - - +
663A ASN* 2.8 46.1 + - - +
664A ASP 3.7 1.8 - - - +
666A PHE* 1.3 76.1 - - - +
668A LEU* 1.3 64.8 + - - +
670A SER* 3.2 7.4 + - - -
671A ALA 3.1 17.2 + - - -
701A SER* 4.4 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 668 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A VAL* 3.7 28.3 - - + -
566A PHE* 4.0 11.9 - - + -
631A ARG* 5.3 4.9 - - + -
632A VAL 3.4 24.2 - - - +
633A ASN* 3.7 22.4 - - + +
639A TRP* 4.0 9.6 - - + -
664A ASP* 2.8 30.0 + - + +
665A ALA* 3.6 5.4 - - - +
667A ASN* 1.3 73.2 - - - +
669A ALA* 1.3 59.4 + - - +
671A ALA 3.2 2.6 + - - -
672A HIS 3.2 4.0 + - - -
673A LYS* 2.9 48.3 + - + +
674A VAL* 3.8 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 669 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A ALA 2.9 16.9 + - - +
666A PHE* 3.5 7.4 - - + +
667A ASN 3.2 0.4 - - - -
668A LEU* 1.3 72.1 - - - +
670A SER* 1.3 66.2 + - - +
672A HIS* 3.0 16.1 + - - -
674A VAL* 3.4 18.7 - - + +
676A VAL* 3.8 38.3 + - + +
679A ALA* 4.3 5.2 - - + -
705A PHE* 6.2 0.4 - - + -
950A TRP* 4.4 7.6 + - + +
954A ASN* 5.3 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 670 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A LEU* 3.2 30.3 - - - +
570A PRO* 4.7 2.8 - - - +
666A PHE 3.2 8.7 + - - -
667A ASN* 3.2 11.2 + - - -
669A ALA* 1.3 78.3 - - - +
671A ALA* 1.3 57.4 + - - +
672A HIS* 3.3 5.9 + - - +
704A TYR* 4.0 19.8 - - - -
705A PHE* 6.0 0.3 - - - -
950A TRP* 3.6 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 671 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A PHE* 3.6 27.1 - - + -
567A LEU 3.3 24.2 - - - +
568A LEU 3.4 8.7 + - - +
570A PRO* 3.6 14.2 - - - +
667A ASN 3.1 3.5 + - - +
668A LEU 3.7 5.2 - - - +
669A ALA 3.2 0.2 - - - -
670A SER* 1.3 78.3 - - - +
672A HIS* 1.3 70.7 + - - +
673A LYS* 3.2 18.4 + - - +
----------------------------------------------------------
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