Contacts of the helix formed by residues 650 - 669 (chain D) in PDB entry 5JA4
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 650 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS* 3.2 30.3 + - - +
648D ASP 4.6 0.9 - - - +
649D LEU* 1.3 77.8 - - - +
651D LEU* 1.3 61.5 + - - +
652D GLU* 3.8 6.6 - - + +
653D THR* 3.5 22.3 + - - +
654D ARG* 3.0 26.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 651 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650D ASP* 1.3 71.2 - - - +
652D GLU* 1.3 69.0 + - - +
654D ARG* 3.1 21.8 + - - +
655D GLN* 2.9 41.2 + - + +
658D ARG* 4.8 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 652 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650D ASP* 3.4 6.8 - - + +
651D LEU* 1.3 79.0 - - - +
653D THR* 1.3 57.3 + - - +
655D GLN* 3.2 8.5 + - + +
656D LYS* 2.9 61.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 653 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS 3.2 25.5 + - - +
13B GLY 4.4 0.2 - - - +
609D GLY 6.0 0.2 - - - +
611D PHE* 4.4 7.9 - - + -
641D TRP* 4.2 13.9 - - + -
649D LEU* 3.6 31.2 - - + -
650D ASP* 3.5 24.6 + - - +
651D LEU 3.2 0.6 - - - -
652D GLU* 1.3 75.7 - - - +
654D ARG* 1.3 64.7 + - - +
656D LYS* 3.3 10.1 + - - +
657D ALA* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 654 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646D ARG* 4.9 12.7 + - - +
649D LEU* 3.7 32.1 - - + -
650D ASP 3.0 25.9 + - - +
651D LEU* 3.4 17.9 - - - +
653D THR* 1.3 75.6 - - - +
655D GLN* 1.3 58.5 + - - +
657D ALA* 3.5 7.3 + - - +
658D ARG* 3.1 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 655 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651D LEU* 2.9 29.3 + - + +
652D GLU* 3.5 10.1 - - + +
654D ARG* 1.3 74.7 - - - +
656D LYS* 1.3 65.3 + - - +
657D ALA 3.0 1.3 - - - -
658D ARG* 3.0 38.8 + - - +
659D ALA* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 656 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611D PHE* 3.9 30.4 - - + +
612D GLU* 2.9 45.6 + - - +
652D GLU* 2.9 49.9 + - + +
653D THR* 3.7 7.4 - - - +
655D GLN* 1.3 75.6 - - - +
657D ALA* 1.3 60.4 + - - +
659D ALA* 3.8 6.7 + - - +
660D MET* 3.2 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 657 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611D PHE* 3.7 25.8 - - + -
638D LEU* 3.8 5.4 - - + +
641D TRP* 4.7 2.5 - - + -
642D VAL* 4.1 23.3 - - + -
649D LEU* 5.2 2.5 - - + -
653D THR 3.0 16.5 + - - +
654D ARG* 3.7 7.4 - - - +
655D GLN 3.0 0.2 - - - -
656D LYS* 1.3 77.6 - - - +
658D ARG* 1.3 59.3 + - + +
660D MET 3.8 0.2 - - - -
661D GLU* 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 658 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651D LEU* 4.8 6.3 - - - +
654D ARG* 3.1 59.9 + - - +
655D GLN* 3.0 37.7 + - - +
657D ALA* 1.3 73.7 - - - +
659D ALA* 1.3 65.2 + - - +
661D GLU* 3.0 6.6 + - - +
662D MET* 2.9 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 659 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615D GLU* 5.5 6.3 - - - +
655D GLN 3.0 15.0 + - - +
656D LYS* 3.8 7.0 - - - +
658D ARG* 1.3 75.6 - - - +
660D MET* 1.3 65.6 + - - +
662D MET* 3.1 4.7 + - - +
663D LEU* 2.9 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 660 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602D LEU* 5.3 1.1 - - - -
606D LEU* 4.2 17.3 - - + -
611D PHE* 4.1 14.8 - - + +
614D ALA* 3.9 24.2 - - + -
615D GLU* 3.9 24.9 + - - +
618D LEU* 4.0 25.8 - - + -
638D LEU* 3.5 18.4 - - + -
656D LYS 3.2 16.4 + - - +
657D ALA 3.9 3.4 - - - +
659D ALA* 1.3 80.2 - - - +
661D GLU* 1.3 61.2 + - - +
663D LEU* 3.6 8.1 - - + +
664D LEU* 3.1 45.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
635D LEU* 3.7 13.5 - - + +
638D LEU* 3.7 20.5 - - + +
639D GLN* 3.2 43.1 + - - +
642D VAL* 4.4 9.4 - - - +
657D ALA 2.8 23.0 + - - +
658D ARG* 3.0 8.4 + - - +
660D MET* 1.3 74.8 - - - +
662D MET* 1.3 65.9 + - + +
665D GLN* 3.4 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 662 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658D ARG* 2.9 19.6 + - + +
659D ALA* 3.9 4.0 - - - +
661D GLU* 1.3 79.8 - - + +
663D LEU* 1.3 65.2 + - - +
665D GLN* 4.0 26.0 - - + +
666D ALA* 3.2 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 663 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615D GLU* 3.6 29.2 - - - +
618D LEU* 3.9 26.0 - - + -
659D ALA* 2.9 20.0 + - + +
660D MET* 3.6 12.6 - - - +
661D GLU 3.2 0.2 - - - -
662D MET* 1.3 77.2 - - - +
664D LEU* 1.3 70.9 + - + +
666D ALA* 3.5 6.0 + - - +
667D ALA* 3.2 19.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 664 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602D LEU* 4.1 25.4 - - + -
606D LEU* 3.8 19.3 - - + -
618D LEU* 5.2 4.3 - - + -
624D VAL* 5.1 10.1 - - + -
634D PRO* 3.9 7.9 - - + +
635D LEU* 3.6 37.9 - - + +
638D LEU* 4.0 13.7 - - + -
660D MET* 3.1 36.1 + - + +
661D GLU 4.3 1.8 - - - +
663D LEU* 1.3 79.7 - - + +
665D GLN* 1.3 60.2 + - - +
667D ALA* 2.9 27.1 + - + +
668D ALA* 3.7 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 665 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635D LEU* 3.7 27.7 - - + +
639D GLN* 4.3 8.0 + - - -
661D GLU* 3.4 19.6 + - - +
662D MET* 4.0 28.7 - - + +
663D LEU 3.4 0.6 - - - -
664D LEU* 1.3 79.5 - - - +
666D ALA* 1.3 59.5 + - - +
667D ALA 3.1 1.3 + - - -
668D ALA* 3.9 9.9 + - - +
669D SER* 4.1 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 666 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662D MET* 3.2 19.3 + - + +
663D LEU* 3.7 6.1 - - - +
664D LEU 3.2 0.6 - - - -
665D GLN* 1.3 77.6 - - - +
667D ALA* 1.3 63.3 + - - +
669D SER* 4.0 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 667 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624D VAL* 4.1 27.4 - - + +
663D LEU* 3.2 12.2 + - + +
664D LEU* 2.9 18.7 + - + +
666D ALA* 1.3 79.4 - - - +
668D ALA* 1.3 68.7 + - - +
669D SER* 3.3 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 668 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624D VAL 6.3 0.6 - - - -
625D THR* 6.4 4.3 - - - +
664D LEU 3.7 4.4 + - - +
665D GLN* 3.9 6.9 + - - +
667D ALA* 1.3 79.9 - - - +
669D SER* 1.3 71.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 669 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665D GLN 4.1 8.3 + - - -
666D ALA* 4.0 13.0 - - - +
667D ALA 3.3 8.4 - - - -
668D ALA* 1.3 85.3 - - - +
----------------------------------------------------------
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