Contacts of the helix formed by residues 640 - 661 (chain D) in PDB entry 5UHO
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 MET 640 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C LEU* 3.8 24.7 - - + -
293C LEU* 4.1 17.5 - - - -
319C GLU 5.4 0.2 - - - -
320C ALA* 4.1 21.5 - - + +
387C TRP* 4.4 17.7 - - + -
391C PHE* 5.0 0.4 - - + -
561D LEU* 4.4 17.0 - - + -
628D LEU* 4.6 15.0 - - + -
636D ILE* 3.6 24.9 - - + +
637D LEU* 2.8 8.3 + - - +
639D ASP* 1.4 84.4 - - - +
641D TYR* 1.4 62.7 + - - +
642D SER* 3.2 3.1 - - - -
643D TYR* 3.0 25.5 + - - +
644D VAL* 3.1 24.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 641 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 3.7 13.8 - - + +
70A GLY* 3.5 39.6 + - - -
71A ARG* 5.2 2.7 - - + +
99A ASP* 4.1 9.5 + - - -
285A ASP* 6.2 1.1 - - + -
288A GLN* 4.4 15.5 - - - -
625D PHE* 3.6 25.6 - + - -
629D SER* 5.6 1.8 - - - -
637D LEU* 2.7 45.4 + - + +
638D TYR* 3.6 20.3 + + + +
640D MET* 1.4 69.3 - - - +
642D SER* 1.4 55.9 + - - +
644D VAL* 4.6 4.5 - - - +
645D TRP* 2.7 71.1 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 642 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLN* 3.9 25.5 + - - +
642B SER* 6.1 1.6 - - - -
288C GLN 4.4 8.3 + - - -
289C LYS* 5.7 0.7 - - - -
638D TYR 5.1 0.6 + - - -
640D MET 3.0 1.2 + - - -
641D TYR* 1.4 80.4 - - - +
643D TYR* 1.4 79.4 + - - +
645D TRP* 3.8 1.7 - - - +
646D ASP* 3.2 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 643 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686B ALA* 5.6 0.9 - - - +
284C ASN* 3.2 9.9 + - - -
288C GLN* 3.1 24.9 + - - -
289C LYS* 3.8 12.6 - - - -
290C ARG 3.4 30.1 - - - -
291C LEU* 3.6 37.0 - - + -
317C GLU* 2.8 45.7 + - + -
565D PHE* 3.2 32.8 - + + -
639D ASP 4.8 1.3 - - - -
640D MET* 3.0 15.4 + - - +
642D SER* 1.4 86.5 + - - +
644D VAL* 1.3 61.5 + - - +
646D ASP* 3.8 4.3 + - - +
647D ILE 3.4 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 644 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C LEU* 5.2 1.1 - - + -
561D LEU* 3.8 21.1 - - + -
565D PHE* 4.1 5.6 - - + -
624D MET* 3.5 31.4 - - + -
625D PHE* 3.7 19.3 - - + -
628D LEU* 4.8 7.2 - - + -
637D LEU* 5.8 3.4 - - + -
640D MET* 3.1 36.4 + - + +
641D TYR* 4.3 3.1 - - - +
643D TYR* 1.3 76.5 - - + +
645D TRP* 1.3 65.3 + - - +
647D ILE* 3.4 7.5 - - + +
648D LYS* 3.3 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 645 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 5.0 17.3 - + + -
285A ASP* 3.4 20.1 + - + -
286A TYR* 3.3 38.8 + - - -
288A GLN* 4.2 10.8 - - + -
625D PHE* 3.8 15.8 - + - -
641D TYR* 2.7 64.2 + + + +
642D SER* 3.8 2.2 - - - +
644D VAL* 1.3 74.1 - - - +
646D ASP* 1.4 74.7 + - - +
648D LYS* 3.3 47.7 - - + +
649D SER* 3.2 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 646 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ASP* 3.9 4.3 - - - +
288A GLN* 3.6 15.1 + - - +
289A LYS* 3.5 49.9 + - - +
686B ALA* 4.9 3.4 - - + -
642D SER* 3.2 22.6 + - - +
643D TYR* 4.2 5.3 - - - +
644D VAL 3.3 0.6 - - - -
645D TRP* 1.4 84.6 - - - +
647D ILE* 1.4 65.1 + - - +
649D SER* 3.0 14.6 + - - -
650D ILE* 3.1 19.4 + - - +
682D ARG* 3.7 14.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 647 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B LEU* 3.8 18.4 - - + -
686B ALA* 3.7 38.2 - - + +
564D LEU* 4.1 21.8 - - + +
565D PHE* 3.5 33.2 - - + -
621D VAL* 4.3 11.4 - - + -
624D MET* 5.2 1.8 - - + -
643D TYR 3.4 3.4 + - - +
644D VAL* 3.4 16.8 - - + +
646D ASP* 1.4 75.8 - - - +
648D LYS* 1.3 59.2 + - - +
650D ILE* 3.6 1.0 + - - -
651D MET* 3.0 55.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 648 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621D VAL* 4.5 10.3 - - - +
622D MET* 3.7 18.3 - - + +
625D PHE* 3.9 37.0 - - + -
644D VAL 3.3 9.8 + - - +
645D TRP* 3.3 62.7 - - + +
646D ASP 3.2 0.2 - - - -
647D ILE* 1.3 82.5 - - + +
649D SER* 1.4 67.2 + - - +
651D MET* 3.6 6.7 - - - +
652D SER* 3.0 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 649 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A TYR 4.1 4.2 + - - -
645D TRP* 3.2 22.3 + - - -
646D ASP* 3.0 11.2 + - - -
648D LYS* 1.4 86.9 + - - +
650D ILE* 1.4 59.9 + - - -
651D MET 3.2 1.3 - - - -
652D SER* 2.9 22.6 + - - -
653D MET* 3.0 27.9 + - - +
682D ARG* 3.5 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 650 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LYS* 3.3 25.1 - - - +
686B ALA* 3.4 38.4 - - + +
689B PHE* 3.7 11.2 - - + -
690B GLN* 3.4 38.1 - - + +
693B LEU* 4.9 4.9 - - + -
646D ASP 3.1 17.0 + - - +
647D ILE 4.2 1.6 - - - +
649D SER* 1.4 72.3 - - - +
651D MET* 1.3 58.3 + - + +
653D MET* 3.3 11.4 + - - +
654D VAL* 2.9 36.4 + - + +
682D ARG* 3.5 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 651 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689B PHE* 3.9 38.8 - - + -
564D LEU* 4.7 6.1 - - + -
578D MET* 3.9 18.8 - - + -
618D CYS* 3.8 22.4 - - - +
621D VAL* 3.7 33.0 - - + -
622D MET* 4.4 2.7 - - + -
647D ILE* 3.0 55.3 + - + +
648D LYS 3.6 5.6 - - - +
650D ILE* 1.3 79.7 - - + +
652D SER* 1.4 55.8 + - - +
654D VAL* 4.2 2.2 - - - -
655D LYS* 3.1 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 652 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622D MET* 3.6 28.9 - - - +
648D LYS* 3.0 17.2 + - - -
649D SER* 2.9 16.0 + - - -
651D MET* 1.4 74.1 - - - +
653D MET* 1.3 61.5 + - - +
655D LYS* 3.7 4.2 + - - +
656D SER* 3.2 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 653 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690B GLN* 6.3 1.1 - - - -
693B LEU* 4.6 14.6 - - + -
649D SER* 3.0 28.1 + - - +
650D ILE* 3.3 13.7 + - - +
652D SER* 1.3 74.8 - - - +
654D VAL* 1.3 54.7 + - - +
655D LYS 3.2 0.2 - - - -
656D SER* 3.1 8.2 + - - -
657D PHE* 2.8 36.1 + - - +
682D ARG* 3.2 39.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 654 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689B PHE* 3.6 34.3 - - + -
693B LEU* 4.0 22.7 - - + -
582D PHE* 3.8 16.8 - - + -
614D PHE* 3.5 32.1 - - + -
618D CYS* 4.2 4.7 - - - -
650D ILE* 2.9 20.5 + - + +
651D MET* 4.0 7.0 - - - +
653D MET* 1.3 76.3 - - - +
655D LYS* 1.4 59.6 + - - +
657D PHE* 3.7 7.9 + - - +
658D VAL* 3.3 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 655 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614D PHE* 5.2 0.4 - - - -
615D GLU* 3.6 39.3 - - + +
618D CYS* 3.7 24.0 - - + -
619D GLY* 5.0 3.8 - - - +
622D MET* 4.8 18.0 - - + +
651D MET 3.1 18.6 + - - +
652D SER* 3.7 7.6 - - - +
653D MET 3.2 0.4 - - - -
654D VAL* 1.4 75.1 - - - +
656D SER* 1.4 57.8 + - - +
658D VAL* 3.5 6.6 + - - +
659D GLN* 3.1 53.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 656 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652D SER* 3.2 13.1 + - - -
653D MET* 3.1 10.2 + - - -
655D LYS* 1.4 74.9 - - - +
657D PHE* 1.3 66.2 + - - +
659D GLN* 3.2 24.2 + - - +
660D TRP* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 657 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693B LEU* 3.7 26.0 - - + -
694B PRO* 3.8 24.2 - - + -
582D PHE* 4.1 9.0 - + - -
586D ARG* 3.8 32.8 - - + -
653D MET 2.8 19.8 + - - +
654D VAL 3.8 5.4 - - - +
656D SER* 1.3 71.6 - - - +
658D VAL* 1.4 52.7 + - - +
660D TRP* 3.2 39.1 + + - -
661D LEU* 2.9 59.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 658 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582D PHE* 4.0 18.2 - - + -
585D LEU* 4.6 11.2 - - + -
607D TRP* 3.6 11.3 - - + -
611D ALA* 3.6 36.1 - - + +
614D PHE* 4.0 22.4 - - + -
615D GLU* 3.7 9.1 - - + +
654D VAL 3.3 17.8 + - - +
655D LYS 3.7 4.5 - - - +
656D SER 3.4 0.2 - - - -
657D PHE* 1.4 69.8 - - - +
659D GLN* 1.4 64.5 + - - +
661D LEU* 3.2 23.7 + - + +
662D GLY* 3.3 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 659 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615D GLU* 3.3 22.1 + - - +
655D LYS* 3.1 49.0 + - - +
656D SER* 3.2 31.0 + - - +
658D VAL* 1.4 74.0 - - - +
660D TRP* 1.4 55.8 - - - +
662D GLY* 3.4 14.6 + - - -
663D CYS* 3.6 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 660 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656D SER 3.2 8.0 + - - +
657D PHE* 3.2 46.5 + + - +
659D GLN* 1.4 73.8 - - - +
661D LEU* 1.4 69.0 + - + +
662D GLY 2.9 5.6 - - - -
663D CYS* 3.0 48.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 661 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582D PHE* 5.5 0.7 - - + -
585D LEU 3.7 7.9 - - - +
586D ARG* 3.8 28.9 - - + +
588D ASN 3.7 19.2 - - - +
589D SER* 6.1 1.3 - - - -
607D TRP* 3.3 24.5 - - + -
657D PHE* 2.9 44.3 + - + +
658D VAL* 3.2 20.1 + - + +
660D TRP* 1.4 84.0 - - + +
662D GLY* 1.3 56.0 + - - +
663D CYS 3.5 1.6 - - - -
----------------------------------------------------------
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