Contacts of the helix formed by residues 658 - 673 (chain D) in PDB entry 3A98
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 ASP 658 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640D LEU* 3.5 11.9 - - - -
656D ALA* 3.2 3.3 - - - +
657D PRO* 1.3 85.2 - - - +
659D LYS* 1.3 58.9 + - - +
660D HIS* 2.8 37.4 + - - +
661D GLU* 2.8 22.5 + - - +
662D TYR* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 659 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LYS* 6.3 2.5 - - + -
54A MSE 4.4 22.3 - - + +
639D GLU* 3.7 18.0 + - + +
640D LEU* 3.4 16.2 - - + +
658D ASP* 1.3 71.3 - - - +
660D HIS* 1.3 61.3 + - - +
662D TYR* 3.3 33.0 - - + -
663D CYS* 2.9 48.9 + - - -
680D ASP* 5.0 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 660 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A MSE 4.2 13.3 - - + +
727B ASN* 4.0 31.4 - - + -
111C LYS* 4.5 14.5 + - - -
555D ARG* 4.1 23.9 + - - -
658D ASP* 2.8 17.4 + - - +
659D LYS* 1.3 76.5 - - - +
661D GLU* 1.3 79.5 + - - +
663D CYS* 3.1 7.3 + - - +
664D ILE* 3.0 27.7 + - + +
681D LEU* 3.9 30.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 661 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C LYS* 5.7 0.3 + - - -
555D ARG* 3.8 21.4 + - - -
560D THR* 3.1 34.2 - - - +
562D PHE* 5.4 0.7 - - + -
656D ALA* 4.1 2.9 - - + -
657D PRO* 3.7 35.4 - - + -
658D ASP* 2.8 24.3 + - - +
660D HIS* 1.3 79.2 - - - +
662D TYR* 1.3 67.7 + - - +
664D ILE* 2.9 10.0 + - - +
665D TRP* 2.9 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 662 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618D THR* 2.6 33.2 + - - +
639D GLU* 3.3 21.2 - - - -
640D LEU* 3.6 24.2 - - + -
641D ALA 4.2 4.9 - - - -
642D PHE* 4.1 14.1 - + + -
656D ALA* 3.4 12.2 - - + +
658D ASP 3.0 16.4 + - - +
659D LYS* 3.3 39.3 - - + +
660D HIS 3.2 0.2 - - - -
661D GLU* 1.3 76.2 - - - +
663D CYS* 1.3 61.0 + - - +
665D TRP* 4.3 0.9 - - - +
666D THR* 2.6 58.0 + - + +
679D SER* 6.1 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 663 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A MSE 4.1 16.2 - - - -
659D LYS* 2.9 42.8 + - - -
660D HIS 3.1 7.9 + - - +
662D TYR* 1.3 81.6 - - - +
664D ILE* 1.3 64.2 + - - +
666D THR* 4.2 2.2 - - - -
667D ASP* 2.6 33.2 + - - +
679D SER* 3.4 31.4 - - - +
680D ASP 4.3 2.2 - - - -
681D LEU* 3.7 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 664 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551D GLN* 4.3 2.0 - - - +
552D ARG* 3.5 26.7 - - - +
555D ARG* 3.5 53.2 - - + +
556D LEU* 4.0 12.2 - - + +
560D THR* 5.7 0.7 - - + -
660D HIS* 3.0 28.8 + - + +
661D GLU* 2.9 16.0 + - - +
663D CYS* 1.3 77.3 - - - +
665D TRP* 1.3 65.5 + - + +
668D GLY* 2.9 24.3 + - - -
681D LEU* 3.4 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 665 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556D LEU* 4.0 40.8 - - + +
560D THR* 2.6 44.9 + - + +
562D PHE* 3.5 21.5 - + - -
577D CYS* 3.4 51.1 - - + -
578D ARG* 4.2 4.5 - - - -
586D LEU* 4.2 11.2 - - + -
642D PHE* 3.8 19.1 - - + -
654D PHE* 4.5 6.1 - + - -
661D GLU* 2.9 28.5 + - - +
662D TYR 4.5 0.7 - - - +
664D ILE* 1.3 81.8 - - + +
666D THR* 1.3 60.4 + - - +
668D GLY 4.2 0.2 - - - +
669D LEU* 2.8 53.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 666 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616D VAL* 5.9 3.8 - - - -
618D THR* 5.9 0.9 - - - -
642D PHE* 5.0 9.7 - - - +
662D TYR* 2.6 51.4 + - + +
663D CYS* 3.8 5.8 - - - -
664D ILE 3.4 0.2 - - - -
665D TRP* 1.3 76.1 - - - +
667D ASP* 1.3 70.8 + - - +
669D LEU* 4.4 2.4 - - - +
670D ASN* 2.7 42.9 + - - +
678D MSE 5.3 5.8 - - + +
679D SER* 4.9 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 667 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552D ARG* 3.1 14.1 + - - +
663D CYS 2.6 17.9 + - - +
666D THR* 1.3 74.6 - - - +
668D GLY* 1.3 61.9 + - - +
670D ASN* 3.6 2.1 - - - +
671D ALA 2.9 24.8 + - - -
677D MSE 3.0 38.0 - - + +
678D MSE 3.3 10.4 + - - -
679D SER* 2.5 48.7 + - - -
682D THR* 3.1 13.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 668 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552D ARG* 4.2 8.3 - - - -
553D LEU* 4.1 4.9 - - - +
556D LEU* 4.1 18.8 - - - -
664D ILE 2.9 17.9 + - - -
665D TRP 3.4 0.9 + - - -
667D ASP* 1.3 76.8 - - - +
669D LEU* 1.3 62.8 + - - +
671D ALA* 3.0 6.4 + - - +
672D LEU* 3.0 22.9 + - - +
677D MSE 3.7 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 669 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556D LEU* 4.2 15.2 - - + +
586D LEU* 4.4 10.1 - - + -
616D VAL* 3.7 26.7 - - + -
642D PHE* 4.0 22.2 - - + -
644D ILE* 3.8 38.8 - - + -
665D TRP* 2.8 36.0 + - + +
666D THR* 4.4 1.8 - - - +
668D GLY* 1.3 70.7 - - - -
670D ASN* 1.3 63.9 + - - +
672D LEU* 3.0 18.9 + - + +
673D LEU* 2.9 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 670 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616D VAL* 4.6 15.4 - - - +
666D THR* 2.7 32.8 + - - +
667D ASP* 3.6 6.5 - - - +
668D GLY 3.2 0.4 - - - -
669D LEU* 1.3 78.4 - - - +
671D ALA* 1.3 58.3 + - - +
673D LEU* 3.1 7.0 + - - -
674D GLY 3.0 4.9 + - - -
675D LYS* 2.6 55.8 + - + +
676D ASP 3.1 28.1 + - - +
677D MSE 5.1 0.2 - - - +
678D MSE 4.9 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 671 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549D LYS* 4.1 35.1 + - + +
553D LEU* 4.8 5.4 - - + -
667D ASP 2.9 18.0 + - - +
668D GLY* 3.4 4.9 - - - +
670D ASN* 1.3 75.7 - - - +
672D LEU* 1.3 59.2 + - - +
674D GLY* 2.8 20.1 + - - -
675D LYS 3.7 9.8 + - - +
677D MSE 3.8 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 672 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553D LEU* 4.1 22.4 - - + -
556D LEU* 4.3 11.2 - - + -
579D LEU* 4.0 26.7 - - + -
583D HIS* 3.9 31.2 - - + +
586D LEU* 5.2 1.8 - - + -
610D VAL* 3.9 29.9 - - + +
668D GLY 3.0 16.3 + - - +
669D LEU* 3.3 21.3 - - + +
671D ALA* 1.3 77.7 - - - +
673D LEU* 1.3 60.4 + - + +
674D GLY 3.3 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 673 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610D VAL* 4.2 11.9 - - + +
611D ALA* 6.0 0.2 - - - -
613D ILE* 3.7 42.0 - - + +
614D LYS 4.8 2.0 - - - +
615D ALA* 4.2 7.4 - - - -
616D VAL* 3.7 37.5 - - + +
669D LEU* 2.9 14.6 + - + +
670D ASN* 3.1 6.7 + - - +
672D LEU* 1.3 78.3 - - + +
674D GLY* 1.3 63.2 + - - +
675D LYS* 3.2 24.3 + - + +
----------------------------------------------------------
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