Contacts of the helix formed by residues 619 - 640 (chain D) in PDB entry 3T6A
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 619 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618D GLY* 1.3 76.8 + - - +
620D LEU* 1.3 65.0 + - - +
621D GLU* 2.7 37.5 + - + +
622D ASP* 2.7 58.4 + - - +
623D ARG* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 620 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618D GLY 4.1 0.4 + - - -
619D THR* 1.3 72.7 + - - +
621D GLU* 1.3 74.8 + - - +
623D ARG* 3.0 45.2 + - - +
624D ALA* 3.1 21.0 + - - +
664D LYS* 3.7 25.1 - - + +
665D THR* 3.5 28.5 - - - +
668D ALA* 4.4 9.4 - - + -
816D GLU* 4.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 621 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619D THR* 2.7 28.0 + - + +
620D LEU* 1.3 93.1 - - - +
622D ASP* 1.3 58.9 + - - +
624D ALA* 3.4 5.1 + - - +
625D ALA* 3.0 26.6 + - - +
668D ALA* 5.6 1.6 - - + -
672D GLN* 4.6 26.6 - - - +
673D TYR* 4.7 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 622 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617D THR* 4.4 4.0 - - + -
618D GLY* 4.4 11.1 + - - +
619D THR* 2.7 44.6 + - + +
621D GLU* 1.3 76.5 - - - +
623D ARG* 1.3 57.2 + - - +
625D ALA* 3.4 10.2 - - + +
626D THR* 2.9 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 623 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613D ILE* 3.6 38.1 - - + +
617D THR* 3.8 21.5 - - + -
618D GLY 4.7 5.1 + - - -
619D THR 2.9 8.4 + - - +
620D LEU* 3.0 42.6 - - - +
621D GLU 3.1 0.2 - - - -
622D ASP* 1.3 76.4 - - - +
624D ALA* 1.3 59.4 + - - +
626D THR* 3.2 2.9 + - - -
627D LEU* 2.9 28.9 + - - +
662D LEU* 5.0 3.6 - - - +
665D THR* 3.0 20.8 + - + +
815D LEU* 3.9 38.5 + - - +
816D GLU* 2.9 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 624 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620D LEU 3.1 7.7 + - - +
621D GLU 3.4 7.8 + - - +
623D ARG* 1.3 74.1 - - - +
625D ALA* 1.3 66.0 + - - +
627D LEU* 3.1 5.7 + - - +
628D SER* 2.8 25.5 + - - -
665D THR* 3.8 9.3 - - - +
668D ALA* 3.7 30.1 - - + -
669D LEU* 3.9 16.3 - - - +
672D GLN* 4.1 3.1 - - - +
673D TYR* 3.9 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 625 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621D GLU 3.0 15.6 + - - +
622D ASP* 3.4 18.2 - - - +
624D ALA* 1.3 77.7 - - - +
626D THR* 1.3 61.4 + - - +
628D SER* 3.3 4.0 + - - -
629D LYS* 3.1 20.8 + - - +
673D TYR* 3.6 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 626 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541D LYS* 2.7 37.6 + - - +
612D ASP* 3.1 23.8 - - - +
613D ILE* 4.3 6.7 - - + -
617D THR* 3.7 5.8 - - - +
622D ASP* 2.9 21.6 + - - +
623D ARG* 3.5 7.4 - - - -
624D ALA 3.2 0.2 - - - -
625D ALA* 1.3 73.8 - - - +
627D LEU* 1.3 65.5 + - - +
629D LYS* 3.0 16.7 + - + +
630D ILE* 3.0 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 627 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613D ILE* 3.9 19.9 - - + +
623D ARG 2.9 16.8 + - - +
624D ALA* 3.5 5.6 - - - +
626D THR* 1.3 76.0 - - - +
628D SER* 1.3 62.0 + - - +
630D ILE* 3.4 6.8 + - - +
631D ILE* 3.1 28.8 + - + +
654D LEU* 3.4 33.0 - - + -
659D ILE* 5.0 2.2 - - + -
665D THR* 4.5 13.9 - - + -
666D TRP* 3.5 50.5 - - + +
669D LEU* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 628 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624D ALA 2.8 17.5 + - - -
625D ALA* 3.4 5.8 - - - -
626D THR 3.1 0.2 - - - -
627D LEU* 1.3 77.4 - - - +
629D LYS* 1.3 61.4 + - - +
631D ILE* 3.3 4.0 + - - +
632D GLN* 3.0 33.3 + - - +
669D LEU* 3.7 10.7 - - - +
673D TYR* 3.5 39.5 - - - +
676D THR* 3.7 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 629 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544D PHE 2.8 24.4 + - - +
545D THR* 4.0 12.8 + - - +
547D ASN 2.6 25.3 + - - -
548D ASP* 4.1 6.9 - - - +
549D PRO* 4.2 9.8 - - + +
552D ILE* 4.1 13.2 - - + -
625D ALA 3.1 11.5 + - - +
626D THR* 3.0 10.8 + - - +
628D SER* 1.3 76.0 - - - +
630D ILE* 1.3 58.3 - - - +
632D GLN* 3.1 19.0 + - - +
633D VAL* 2.8 34.8 + - + +
834D UNX 3.1 23.1 - - - -
835D UNX 4.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 630 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609D ILE* 3.7 31.4 - - + +
612D ASP* 4.3 3.8 - - - +
613D ILE* 3.6 34.5 - - + -
626D THR* 3.0 21.8 + - + +
627D LEU* 3.6 8.1 - - - +
629D LYS* 1.3 77.1 - - - +
631D ILE* 1.3 62.1 + - - +
633D VAL* 3.3 5.1 + - - -
634D ALA* 3.0 22.2 + - - +
650D LEU* 3.7 18.7 - - + +
654D LEU* 3.9 26.2 - - + -
835D UNX 4.2 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 631 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627D LEU* 3.1 17.0 + - + +
628D SER 3.3 1.5 + - - +
630D ILE* 1.3 75.7 - - - +
632D GLN* 1.3 57.5 + - - +
634D ALA* 3.3 7.0 + - - +
635D VAL* 2.9 32.9 + - + +
654D LEU* 4.0 20.0 - - + -
666D TRP* 4.7 5.8 - - + -
669D LEU* 4.1 20.2 - - + -
676D THR* 3.5 42.6 - - + +
679D LEU* 5.2 1.8 - - + -
680D TYR* 3.7 33.9 - - + +
684D LEU* 4.0 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 632 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549D PRO* 3.6 27.1 - - + +
628D SER* 3.0 23.8 + - - +
629D LYS* 3.1 19.5 + - - +
631D ILE* 1.3 77.0 - - - +
633D VAL* 1.3 63.1 + - - +
635D VAL* 3.2 11.0 + - - +
636D GLU* 3.0 24.6 + - - +
676D THR* 4.3 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 633 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549D PRO* 3.7 31.6 - - + +
552D ILE* 4.0 36.8 - - + -
553D ALA* 4.5 5.2 - - - +
556D VAL* 5.7 2.5 - - + -
629D LYS* 2.8 28.4 + - + +
630D ILE* 3.7 6.3 - - - +
632D GLN* 1.3 71.2 - - - +
634D ALA* 1.3 58.3 + - - +
636D GLU* 3.2 6.2 + - - +
637D LEU* 2.9 35.3 + - + +
650D LEU* 3.9 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 634 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630D ILE* 3.0 18.1 + - + +
631D ILE* 3.6 7.9 - - - +
633D VAL* 1.3 74.2 - - - +
635D VAL* 1.3 65.1 + - - +
637D LEU* 3.4 6.5 + - - +
638D LYS* 3.1 18.9 + - - +
647D PHE* 3.4 26.9 - - + -
650D LEU* 3.8 24.0 - - + +
651D MET* 4.9 6.1 - - - -
654D LEU* 5.7 1.6 - - + -
684D LEU* 4.4 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 635 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631D ILE* 2.9 22.0 + - + +
632D GLN* 3.2 10.5 + - - +
634D ALA* 1.3 75.0 - - - +
636D GLU* 1.3 64.7 + - - +
638D LYS* 3.4 4.5 + - - +
639D ASP* 2.9 45.8 + - + +
679D LEU* 3.8 32.3 - - + -
684D LEU* 4.0 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 636 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549D PRO* 3.9 7.4 - - + +
550D LYS* 2.9 61.0 + - - +
553D ALA* 3.6 17.5 - - + -
632D GLN 3.0 17.0 + - - +
633D VAL 3.2 9.4 + - - +
635D VAL* 1.3 78.3 - - + +
637D LEU* 1.3 60.8 + - - +
640D SER* 2.8 41.5 + - - -
641D MET* 3.0 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 637 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553D ALA* 3.9 31.2 - - + +
556D VAL* 4.0 19.1 - - + -
633D VAL* 2.9 23.8 + - + +
634D ALA* 3.4 6.9 + - - +
636D GLU* 1.3 73.1 - - - +
638D LYS* 1.3 59.0 + - - +
641D MET* 3.5 4.7 - - + -
642D GLY 2.8 25.5 + - - -
643D ASP* 2.8 37.9 + - + +
646D SER* 3.9 29.6 - - - +
647D PHE* 3.9 6.3 - - + +
650D LEU* 4.0 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 638 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634D ALA 3.1 16.6 + - - +
635D VAL* 3.7 3.6 - - - +
637D LEU* 1.3 80.8 - - - +
639D ASP* 1.3 92.6 + - - +
642D GLY* 3.4 11.9 + - - -
643D ASP 4.9 0.7 - - - +
644D LEU* 4.9 3.4 - - - -
647D PHE* 3.9 15.7 - - + -
683D GLN* 5.3 5.3 - - - +
684D LEU* 4.2 23.6 - - + +
687D PHE* 3.5 57.4 - - + -
701D PRO* 3.1 27.1 - - + +
702D PRO* 4.8 4.2 - - - +
703D ASN 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 639 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635D VAL* 2.9 33.9 + - + +
636D GLU* 5.4 0.2 - - - -
638D LYS* 1.3 111.7 + - - +
640D SER* 1.3 60.2 + - - +
684D LEU* 6.0 0.9 - - - +
702D PRO* 3.3 34.1 - - + +
703D ASN* 3.4 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 640 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550D LYS* 3.2 17.9 + - - -
636D GLU* 2.8 46.7 + - - -
639D ASP* 1.3 76.7 - - - +
641D MET* 1.3 71.3 + - - +
642D GLY 3.5 0.4 - - - -
703D ASN* 2.7 30.1 + - - +
764D ILE* 3.6 7.6 - - - +
----------------------------------------------------------
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