Contacts of the helix formed by residues 747 - 764 (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 747 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676D ASP 4.8 1.6 - - - +
677D LEU* 3.2 23.1 - - - +
679D GLY* 4.4 12.3 - - - +
680D ASN* 5.7 1.8 - - - +
688D VAL* 3.8 21.9 - - + +
742D ILE* 4.0 18.5 - - + +
745D SER* 3.6 12.6 - - - +
746D VAL* 1.3 83.6 - - - +
748D TRP* 1.3 59.4 + - - +
749D ALA* 3.0 21.2 + - - +
750D ASP* 2.9 34.0 + - - +
751D PHE* 3.5 3.5 + - - -
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Residues in contact with TRP 748 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617D ILE* 3.7 16.2 - - + +
621D ILE* 4.3 7.9 - - + -
665D LEU* 3.8 26.2 - - + -
668D ALA* 3.5 24.9 - - + -
669D ARG* 4.0 23.6 - - + +
672D THR* 3.6 36.0 + - + -
677D LEU* 3.0 33.4 + - + +
678D ALA* 4.3 5.2 + - - +
688D VAL* 3.4 20.0 - - + +
689D ASP* 3.9 19.8 + - - -
692D VAL* 3.8 35.2 - - + -
747D THR* 1.3 74.3 - - - +
749D ALA* 1.3 56.5 + - - +
750D ASP 3.2 0.2 - - - -
751D PHE* 3.4 19.9 - - + +
752D TYR* 2.9 28.0 + + + +
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Residues in contact with ALA 749 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688D VAL* 3.9 21.3 - - + +
691D ILE* 4.3 9.0 - - + -
692D VAL* 3.9 13.9 - - + -
695D LEU* 4.4 2.8 - - - +
741D LEU* 3.8 5.7 - - + +
742D ILE* 3.7 23.6 - - + -
747D THR* 3.0 13.3 + - - +
748D TRP* 1.3 77.8 - - - +
750D ASP* 1.3 61.4 + - - +
752D TYR* 3.3 2.6 + - - +
753D TRP* 3.0 27.7 + - - +
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Residues in contact with ASP 750 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740D TRP* 3.5 17.0 - - - +
741D LEU* 3.0 40.8 + - - +
742D ILE 4.9 0.3 + - - -
745D SER 4.2 0.2 - - - +
746D VAL* 3.4 13.5 - - + -
747D THR* 2.9 36.0 + - - +
749D ALA* 1.3 74.9 - - - +
751D PHE* 1.3 65.9 + - - +
753D TRP* 3.2 4.8 + - - +
754D GLU* 3.1 22.9 + - - +
777D LEU* 3.7 9.2 - - + +
781D VAL* 3.8 22.0 - - + +
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Residues in contact with PHE 751 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617D ILE* 3.6 12.3 - - + -
620D TYR* 3.9 30.3 - + + -
621D ILE* 4.5 6.3 - - + -
624D TYR* 3.6 35.4 - + + -
677D LEU* 3.8 27.6 - - + -
746D VAL* 3.8 18.6 - - + -
747D THR 4.2 3.4 - - - -
748D TRP* 3.4 22.4 - - + +
749D ALA 3.3 0.2 - - - -
750D ASP* 1.3 79.7 - - - +
752D TYR* 1.3 58.0 + - - +
754D GLU* 3.3 3.5 + - - +
755D ILE* 2.9 32.9 + - - +
781D VAL* 3.7 18.8 - - + -
784D ILE* 4.0 8.1 - - + -
787D VAL* 3.9 20.0 - - + -
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Residues in contact with TYR 752 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614D ARG* 4.2 4.2 + - - +
617D ILE* 3.8 31.6 - - + +
664D SER* 5.2 0.5 + - - -
665D LEU* 3.9 18.8 - - + +
692D VAL* 3.6 40.4 - - + -
695D LEU* 3.8 16.2 - - + -
696D ASP* 2.6 33.7 + - + -
748D TRP* 2.9 17.2 + + - +
749D ALA* 3.6 8.7 - - - +
750D ASP 3.2 0.4 - - - -
751D PHE* 1.3 74.8 - - - +
753D TRP* 1.3 60.1 + - - +
755D ILE* 3.8 8.5 - - + +
756D CYS* 2.9 47.7 + - - -
3801D O16 3.2 26.8 - + - -
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Residues in contact with TRP 753 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695D LEU* 3.7 21.9 - - + +
728D MET* 3.5 33.7 - - + -
731D LEU* 3.6 28.0 - - + -
741D LEU* 4.0 14.6 - - + -
749D ALA 3.0 14.0 + - - +
750D ASP* 3.5 7.9 - - - +
752D TYR* 1.3 75.3 - - - +
754D GLU* 1.3 53.5 + - - +
756D CYS* 4.8 2.0 - - + -
757D SER* 2.7 67.0 + - - -
760D LEU* 5.5 3.1 - - + -
767D LEU* 5.0 0.4 - - + -
768D LEU* 4.1 10.5 - - + -
774D LEU* 3.3 48.9 + - + +
777D LEU* 3.7 28.0 - - + -
778D ARG* 3.7 11.7 - - + +
781D VAL* 6.1 0.2 - - + -
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Residues in contact with GLU 754 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620D TYR* 2.6 37.5 + - - -
750D ASP 3.1 9.4 + - - +
751D PHE 3.6 6.3 - - - +
752D TYR 3.3 0.2 - - - -
753D TRP* 1.3 81.8 - - + +
755D ILE* 1.3 57.0 + - - +
757D SER* 3.6 5.2 - - - -
758D THR* 2.9 44.0 + - - -
778D ARG* 3.2 34.1 + - - +
781D VAL* 3.9 19.5 - - + -
782D GLN* 2.8 32.5 + - + +
791D ILE* 4.2 3.4 - - - +
794D ARG* 5.3 2.3 + - - -
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Residues in contact with ILE 755 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D ARG* 5.4 5.4 + - + +
613D GLY 4.5 9.2 - - - +
616D GLU* 3.7 22.7 - - + -
617D ILE* 3.4 42.4 - - + +
620D TYR* 3.5 37.7 - - + +
751D PHE 2.9 20.6 + - - +
752D TYR* 3.8 10.3 - - + +
753D TRP 3.3 0.2 - - - -
754D GLU* 1.3 76.7 - - - +
756D CYS* 1.3 67.8 + - - +
758D THR* 3.3 13.5 + - - +
759D THR* 3.4 15.1 + - - +
3801D O16 4.6 10.3 - - + -
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Residues in contact with CYS 756 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695D LEU* 4.2 11.4 - - + -
699D MET* 3.6 39.2 - - - +
752D TYR* 2.9 49.1 + - - +
753D TRP* 4.0 7.9 - - + +
755D ILE* 1.3 77.0 - - - +
757D SER* 1.3 58.0 + - - +
759D THR* 3.1 7.0 + - - -
760D LEU* 3.0 33.3 + - + +
3801D O16 3.7 11.2 - - - -
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Residues in contact with SER 757 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753D TRP* 2.7 54.6 + - - -
754D GLU 3.4 0.3 + - - -
756D CYS* 1.3 73.9 - - - +
758D THR* 1.3 59.5 + - - +
760D LEU* 4.3 8.5 - - - +
761D LEU* 2.9 36.0 + - - +
767D LEU* 4.8 2.5 - - - -
768D LEU* 4.5 5.4 - - - -
778D ARG* 2.9 39.2 + - - +
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Residues in contact with THR 758 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D ARG* 4.1 26.0 - - - +
620D TYR* 5.3 0.8 + - - -
754D GLU* 2.9 34.5 + - - -
755D ILE* 3.5 7.2 - - - -
756D CYS 3.2 0.2 - - - -
757D SER* 1.3 78.4 + - - +
759D THR* 1.3 62.7 + - - +
761D LEU* 3.6 7.8 + - - +
762D VAL* 3.4 19.7 + - + +
778D ARG* 3.1 19.1 + - - +
782D GLN* 4.3 0.7 + - - -
794D ARG* 4.9 11.1 + - - +
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Residues in contact with THR 759 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D ARG* 3.3 21.0 + - - +
613D GLY* 5.7 0.5 + - - -
699D MET* 4.3 9.6 - - + -
704D TRP* 3.8 30.1 - - + -
755D ILE* 3.4 9.7 + - - +
756D CYS 3.1 8.5 + - - -
758D THR* 1.3 77.0 - - - +
760D LEU* 1.3 66.5 + - - +
762D VAL* 3.0 24.2 + - - +
763D PHE* 3.3 15.7 - - + -
799D LEU* 4.3 15.7 + - + +
3801D O16 5.4 9.4 - - + +
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Residues in contact with LEU 760 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698D PHE* 4.2 18.6 - - + -
699D MET* 3.7 32.1 - - + -
702D PHE* 3.9 29.4 - - + -
704D TRP* 5.2 2.7 - - + -
720D LEU* 4.4 8.1 - - + +
727D LEU* 6.1 0.2 - - + -
728D MET* 4.8 10.5 - - + -
753D TRP* 5.5 2.5 - - + -
756D CYS* 3.0 22.8 + - + +
757D SER* 4.0 3.6 - - - +
759D THR* 1.3 78.5 - - + +
761D LEU* 1.3 58.8 + - - +
763D PHE* 3.1 10.2 + - + +
764D LYS* 2.9 28.4 + - - +
767D LEU* 3.8 28.0 - - + -
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Residues in contact with LEU 761 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757D SER 2.9 25.4 + - - +
758D THR* 3.7 5.8 - - - +
759D THR 3.2 0.2 - - - -
760D LEU* 1.3 74.2 - - - +
762D VAL* 1.3 66.2 + - - +
763D PHE 3.2 0.2 - - - -
764D LYS 3.7 9.2 - - - +
765D PRO* 3.4 46.1 - - + +
767D LEU* 3.9 17.5 - - + +
768D LEU* 4.3 16.2 - - + +
778D ARG* 3.4 39.5 - - - +
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Residues in contact with VAL 762 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D ARG* 4.8 2.2 - - - +
758D THR* 3.4 18.6 - - + +
759D THR* 3.0 16.6 + - + +
761D LEU* 1.3 81.5 - - - +
763D PHE* 1.3 77.9 + - + +
765D PRO* 4.5 6.9 - - - +
798D LYS* 4.3 35.9 - - + +
799D LEU* 5.6 0.2 - - + -
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Residues in contact with PHE 763 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702D PHE* 6.4 0.2 - + - -
704D TRP* 4.2 5.4 - + - -
712D LYS* 6.2 2.2 - - - -
716D PHE* 3.8 38.1 - + + -
717D ASN* 4.8 8.4 - - - +
720D LEU* 3.7 23.5 - - + +
759D THR* 3.3 26.2 - - + -
760D LEU* 3.1 7.6 + - + +
762D VAL* 1.3 90.4 - - + +
764D LYS* 1.3 62.4 + - - +
765D PRO* 3.8 5.5 - - - +
798D LYS* 4.6 18.8 - - - -
799D LEU* 3.7 33.4 - - + -
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Residues in contact with LYS 764 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717D ASN* 6.1 1.9 - - - +
720D LEU* 3.7 40.8 - - + +
721D THR* 3.1 30.3 + - - +
760D LEU 2.9 8.2 + - - +
761D LEU* 3.5 9.4 - - - -
763D PHE* 1.3 82.1 - - - +
765D PRO* 1.3 68.5 - - + +
766D ASP* 3.2 30.9 + - - +
767D LEU* 3.0 32.9 + - + +
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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) + - + + + + + -
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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