Contacts of the helix formed by residues 681 - 700 (chain D) in PDB entry 1V40
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 681 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679D GLY 3.4 1.0 + - - -
680D ASN* 1.3 85.2 - - + +
682D GLU* 1.3 59.7 + - - +
683D MET* 3.5 6.4 + - - +
684D GLU* 2.9 41.2 + - - +
685D GLN* 2.8 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 682 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 3.6 29.0 - - + +
73A LYS* 5.0 10.1 + - + +
74A ASN* 3.2 27.8 + - - -
681D THR* 1.3 72.9 - - - +
683D MET* 1.3 63.3 + - - +
685D GLN* 3.4 17.3 + - - +
686D CYS 3.2 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 683 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 5.0 11.4 - - + -
59A LEU* 3.3 45.5 - - + -
61A LEU* 3.8 24.0 - - + -
70A TYR* 3.6 28.7 - - + +
681D THR* 3.1 6.3 + - - +
682D GLU* 1.3 78.2 - - - +
684D GLU* 1.3 61.5 + - + +
686D CYS* 3.1 7.2 + - - +
687D HIS* 3.0 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 684 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679D GLY* 4.6 0.4 - - - -
680D ASN* 3.5 30.8 + - - +
681D THR* 2.9 36.8 + - + +
683D MET* 1.3 75.4 - - + +
685D GLN* 1.3 59.7 + - - +
687D HIS* 3.1 15.3 + - + +
688D VAL* 2.9 33.0 + - - +
742D ILE* 3.6 13.0 - - + +
743D GLY* 3.5 31.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 685 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LYS* 4.1 24.4 - - - +
678D ALA* 3.4 34.5 - - + +
679D GLY 3.3 21.0 + - - +
680D ASN 5.1 0.6 - - - -
681D THR* 2.8 21.6 + - - +
682D GLU* 3.5 17.5 - - - +
684D GLU* 1.3 76.2 - - - +
686D CYS* 1.3 63.4 + - - +
688D VAL* 3.3 2.9 + - - +
689D ASP* 3.1 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 686 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 4.1 29.8 - - + -
62A HIS 4.8 2.7 - - - -
66A ALA* 3.5 29.6 - - - +
67A ILE* 4.1 4.5 - - - -
70A TYR* 3.9 21.8 - - + -
73A LYS* 4.9 2.4 - - - +
682D GLU 3.2 11.5 + - - +
683D MET* 3.1 11.4 + - - +
684D GLU 3.1 0.4 - - - -
685D GLN* 1.3 78.2 - - - +
687D HIS* 1.3 58.8 + - - +
689D ASP* 3.2 9.6 + - - +
690D ALA* 2.8 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 687 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR 3.7 15.0 - - - -
61A LEU* 3.4 32.5 - - + +
62A HIS* 5.1 9.0 + - - -
683D MET* 3.0 38.0 + - + +
684D GLU* 3.1 17.0 + - + +
686D CYS* 1.3 73.8 - - - +
688D VAL* 1.3 59.5 + - - +
690D ALA* 3.6 5.3 - - - +
691D ILE* 2.9 34.7 + - - +
734D TYR* 3.6 25.6 + + - +
742D ILE* 3.8 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 688 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678D ALA 3.6 16.6 - - - +
679D GLY* 4.4 0.9 - - - -
684D GLU 2.9 19.8 + - - +
685D GLN 3.5 7.9 - - - +
687D HIS* 1.3 77.5 - - - +
689D ASP* 1.3 64.3 + - - +
691D ILE* 3.3 1.7 + - - +
692D VAL* 3.0 27.8 + - + +
742D ILE* 4.0 15.9 - - + +
747D THR* 3.8 27.6 - - + +
748D TRP* 3.4 41.3 - - + +
749D ALA* 3.9 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 689 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ALA* 3.7 15.5 - - + +
69A ARG* 3.2 30.5 + - - +
73A LYS* 3.9 9.5 + - - -
669D ARG* 2.8 35.7 + - - +
685D GLN* 3.1 15.3 + - - +
686D CYS* 3.2 8.9 + - - +
688D VAL* 1.3 81.3 - - - +
690D ALA* 1.3 57.7 + - - +
692D VAL* 3.4 7.0 + - - +
693D ASP* 3.0 33.7 + - - +
748D TRP* 3.9 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 690 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A HIS* 3.4 48.9 - - + +
63A GLN* 3.3 12.3 - - + +
66A ALA* 3.6 3.5 - - + +
686D CYS* 2.8 18.2 + - - +
687D HIS* 3.6 7.2 - - - +
688D VAL 3.2 0.2 - - - -
689D ASP* 1.3 75.1 - - - +
691D ILE* 1.3 65.7 + - - +
693D ASP 3.4 0.3 + - - -
694D THR* 3.0 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 691 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 3.6 38.1 - - + -
62A HIS* 4.3 4.9 - - + +
687D HIS 2.9 22.9 + - - +
688D VAL 3.9 3.1 - - - +
690D ALA* 1.3 71.9 - - - +
692D VAL* 1.3 63.7 + - - +
694D THR* 3.3 4.9 + - - -
695D LEU* 3.0 41.0 + - + +
731D LEU* 4.7 8.7 - - + -
734D TYR* 3.7 24.9 - - + +
741D LEU* 4.0 20.9 - - + -
742D ILE* 3.8 19.1 - - + -
749D ALA* 4.3 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 692 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665D LEU* 3.5 37.5 - - + -
669D ARG* 5.3 1.8 - - - +
688D VAL 3.0 22.0 + - - +
689D ASP* 3.6 4.7 - - - +
691D ILE* 1.3 77.2 - - - +
693D ASP* 1.3 59.4 + - - +
695D LEU* 3.3 1.6 + - - -
696D ASP* 2.9 26.5 + - - +
748D TRP* 3.8 31.9 - - + -
749D ALA* 3.9 24.5 - - - -
752D TYR* 3.6 21.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 693 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLN* 3.6 26.7 - - + +
65A LEU* 4.0 26.9 - - - +
66A ALA* 4.6 5.4 + - - +
69A ARG* 5.4 3.1 + - - -
93A ASP* 5.1 4.6 - - - +
3900A MG 4.2 12.7 - - - -
665D LEU* 3.6 20.1 - - - +
669D ARG* 4.8 7.6 + - - -
689D ASP* 3.0 19.9 + - - +
690D ALA 4.0 0.2 - - - +
692D VAL* 1.3 75.7 - - - +
694D THR* 1.3 60.9 + - - +
696D ASP* 3.8 3.8 - - - +
697D ASP* 2.8 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 694 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 3.8 34.1 - - + +
62A HIS* 3.5 17.9 + - - -
63A GLN* 3.1 16.8 + - - +
690D ALA 3.0 17.7 + - - -
691D ILE* 3.3 8.3 + - - +
693D ASP* 1.3 76.9 - - - +
695D LEU* 1.3 66.1 + - + +
697D ASP* 3.6 4.4 - - - +
698D PHE* 3.3 20.3 + - - +
727D LEU* 3.8 17.7 - - + +
731D LEU* 5.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 695 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691D ILE* 3.0 36.1 + - + +
692D VAL* 3.6 4.3 - - - +
694D THR* 1.3 76.8 - - - +
696D ASP* 1.3 61.6 + - - +
698D PHE* 3.2 7.0 + - - +
699D MET* 3.0 27.4 + - - +
727D LEU* 4.6 10.8 - - + -
728D MET* 5.8 0.2 - - + -
731D LEU* 3.8 33.0 - - + -
741D LEU* 5.4 0.4 - - + -
749D ALA 4.4 0.4 - - - +
752D TYR* 3.8 20.9 - - + +
753D TRP* 3.7 46.4 - - + +
756D CYS* 4.2 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 696 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP* 5.4 1.4 - - - +
3900A MG 4.0 11.8 - - - -
614D ARG* 2.8 30.8 + - - -
665D LEU* 3.7 22.3 - - + +
692D VAL 2.9 17.3 + - - +
693D ASP* 3.8 4.9 - - - +
695D LEU* 1.3 73.5 - - - +
697D ASP* 1.3 60.9 + - - +
699D MET* 3.7 3.8 - - - +
700D SER* 2.8 37.9 + - - -
752D TYR* 2.6 29.5 + - - +
3800D GSH 4.9 5.4 + - - -
3801D O16 3.4 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 697 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLN* 3.1 14.0 + - - -
96A ASP* 5.3 1.0 - - - +
100A SER* 5.7 0.5 + - - -
3200A GSH 2.7 35.6 + - - +
3900A MG 4.1 16.1 - - - -
693D ASP* 2.8 27.8 + - - +
694D THR* 3.6 6.3 - - - +
696D ASP* 1.3 75.4 - - - +
698D PHE* 1.3 62.9 + - - +
700D SER* 3.4 12.9 + - - -
701D CYS* 3.5 16.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 698 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694D THR 3.3 4.5 + - - +
695D LEU 3.2 7.8 + - - +
697D ASP* 1.3 78.0 - - - +
699D MET* 1.3 67.5 + - - +
701D CYS* 3.0 28.6 + - + +
702D PHE* 3.3 39.4 - + - -
719D LEU* 3.9 11.4 - - + -
720D LEU* 4.7 0.2 - - + -
723D ASN* 3.9 24.5 - - + -
724D ALA* 3.7 35.2 - - + -
727D LEU* 3.7 34.5 - - + -
728D MET* 5.3 0.7 - - + -
760D LEU* 4.2 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 699 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614D ARG* 4.9 0.9 - - - -
695D LEU 3.0 16.6 + - - +
696D ASP 3.2 4.7 + - - +
698D PHE* 1.3 78.3 - - - +
700D SER* 1.3 57.5 + - - +
701D CYS 3.1 4.0 + - - -
702D PHE* 3.3 9.6 + - - -
704D TRP* 2.9 49.1 + - + -
756D CYS* 3.6 36.6 - - - +
759D THR* 4.3 6.3 - - + -
760D LEU* 3.7 39.0 - - + -
3801D O16 3.4 43.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 700 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP* 5.8 0.3 + - - -
614D ARG* 2.9 23.7 + - - +
696D ASP* 2.8 25.3 + - - -
697D ASP* 3.7 8.7 - - - -
698D PHE 3.2 0.8 - - - -
699D MET* 1.3 75.3 - - - +
701D CYS* 1.3 59.6 + - - +
702D PHE 3.3 5.6 + - - +
704D TRP* 4.8 3.3 - - - +
----------------------------------------------------------
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