Contacts of the helix formed by residues 615 - 631 (chain A) in PDB entry 5OQN
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 ALA 615 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A ASN* 2.8 11.8 + - - +
614A THR* 1.3 79.1 + - - +
616A PRO* 1.3 71.4 - - + +
617A ASN* 3.5 17.3 - - - +
618A ILE* 4.0 18.0 - - + +
619A ARG* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 616 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A THR 3.9 6.1 - - - +
615A ALA* 1.3 83.5 - - + +
617A ASN* 1.3 62.5 + - - +
619A ARG* 2.9 10.9 + - + +
620A GLU* 2.8 42.7 + - + +
652A ASN* 4.1 23.6 - - - +
654A SER* 6.0 0.2 - - - -
655A LEU* 6.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 617 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A VAL* 4.8 13.9 - - + +
615A ALA* 3.5 11.3 - - - +
616A PRO* 1.3 79.7 - - - +
618A ILE* 1.3 90.8 + - - +
620A GLU* 3.4 13.1 + - - +
621A LEU* 3.0 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 618 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A SER* 3.7 37.2 - - - +
575A ILE* 4.0 22.2 - - + -
576A VAL* 3.9 18.8 - - + +
579A LEU* 4.3 1.6 - - + -
610A ALA* 3.8 13.1 - - + +
613A ASN* 3.4 37.9 - - + +
615A ALA* 4.0 15.3 - - + +
616A PRO 3.2 0.6 - - - -
617A ASN* 1.3 96.2 + - - +
619A ARG* 1.3 63.3 + - - +
621A LEU* 3.3 9.7 + - - +
622A GLY* 2.9 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 619 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A ALA 3.5 8.7 - - - +
611A VAL* 2.8 45.4 + - + +
612A ARG* 4.8 1.6 - - - +
613A ASN 3.2 23.5 + - - +
614A THR* 4.7 3.1 - - - +
615A ALA 3.0 18.6 + - - +
616A PRO* 2.9 12.7 + - + +
618A ILE* 1.3 76.3 - - - +
620A GLU* 1.3 64.4 + - - +
622A GLY* 2.8 13.0 + - - -
623A VAL* 3.0 19.2 + - + +
647A CYS* 3.7 19.1 - - - +
651A GLY* 5.6 1.6 - - - -
655A LEU* 3.1 37.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 620 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A PRO* 2.8 32.3 + - + +
617A ASN* 3.7 11.2 + - - +
619A ARG* 1.3 70.9 - - - +
621A LEU* 1.3 59.4 + - + +
623A VAL* 3.1 6.9 + - - +
624A LYS* 2.9 28.2 + - - +
654A SER* 2.8 39.6 - - - +
655A LEU* 4.0 21.8 + - + +
658A ILE* 4.1 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 621 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A VAL* 3.8 37.2 - - + +
579A LEU* 4.1 14.8 - - + -
580A THR* 3.8 30.1 - - + +
583A SER* 5.3 0.4 - - - +
617A ASN* 3.0 25.4 + - + +
618A ILE* 3.6 9.4 - - - +
619A ARG 3.2 0.2 - - - -
620A GLU* 1.3 76.0 - - + +
622A GLY* 1.3 60.3 + - - +
624A LYS* 3.1 24.2 + - + +
625A ASN* 2.4 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 622 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A LEU* 4.7 1.8 - - - -
607A ILE* 4.1 8.7 - - - +
610A ALA* 3.8 25.3 - - - +
611A VAL* 4.0 10.8 - - - +
618A ILE 2.9 7.3 + - - -
619A ARG 2.8 14.3 + - - -
621A LEU* 1.3 72.0 - - - +
623A VAL* 1.3 54.4 + - - -
625A ASN* 3.6 4.2 + - - -
626A LEU* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 623 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A VAL* 4.8 13.5 - - + -
619A ARG* 3.0 18.1 + - + +
620A GLU 3.7 4.7 - - - +
622A GLY* 1.3 72.8 - - - +
624A LYS* 1.3 57.3 + - - +
626A LEU* 4.0 6.3 - - + -
627A GLY* 2.7 32.9 + - - -
644A LEU* 3.4 32.5 - - + -
647A CYS* 5.5 6.3 - - + -
655A LEU* 3.7 24.0 - - + -
658A ILE* 4.6 5.4 - - + -
659A ALA* 4.2 13.7 - - + -
662A VAL* 3.9 13.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 624 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A GLU* 5.3 4.4 + - - -
583A SER* 4.2 27.1 + - - +
584A TYR* 5.1 14.1 + - - -
620A GLU 2.9 13.2 + - - +
621A LEU* 3.1 26.2 + - + +
623A VAL* 1.3 78.2 - - - +
625A ASN* 1.3 63.4 + - - +
627A GLY* 3.2 1.6 + - - -
628A LEU* 3.1 28.9 + - + +
658A ILE* 4.3 27.4 - - + +
662A VAL* 4.9 3.8 - - - -
514B ILE* 4.5 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 625 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A LEU* 2.8 31.1 + - + +
582A SER* 2.3 28.3 + - - +
583A SER* 2.9 18.1 + - - -
586A LEU* 3.9 3.1 - - + +
607A ILE* 3.8 23.1 - - + -
621A LEU* 2.4 42.7 + - - +
622A GLY 4.1 1.1 - - - +
624A LYS* 1.3 73.2 - - - +
626A LEU* 1.3 63.5 + - - +
628A LEU* 3.0 11.8 + - - +
629A CYS* 3.0 27.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 626 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A MET* 4.8 7.6 - - - -
607A ILE* 4.1 16.5 - - + +
611A VAL* 4.0 22.9 - - + -
612A ARG* 6.1 0.7 - - - +
622A GLY 2.8 19.5 + - - +
623A VAL* 3.2 7.4 + - + +
625A ASN* 1.3 77.6 - - - +
627A GLY* 1.3 57.2 + - - +
629A CYS* 3.2 4.9 + - - +
630A CYS* 2.9 46.1 + - - -
636A LEU* 4.7 8.7 - - + -
640A ASN* 3.5 34.1 - - + +
643A ILE* 5.1 5.4 - - + -
644A LEU* 4.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 627 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A VAL 2.7 16.6 + - - -
624A LYS 3.7 2.0 - - - -
626A LEU* 1.3 73.3 - - - +
628A LEU* 1.3 62.3 + - - +
630A CYS* 3.0 15.9 + - - +
631A LEU* 3.1 18.4 + - - +
662A VAL* 3.4 31.7 - - - +
666A ILE* 5.0 0.5 - - - +
514B ILE* 3.8 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 628 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A SER* 3.5 45.5 - - - +
586A LEU* 3.7 20.1 - - + +
587A GLU* 4.3 16.4 - - + -
624A LYS* 3.1 20.1 + - + +
625A ASN* 3.0 10.6 + - - +
627A GLY* 1.3 75.2 - - - +
629A CYS* 1.3 61.5 + - - +
631A LEU* 3.7 6.0 + - + +
632A LEU* 3.4 25.5 - - - +
514B ILE* 3.8 40.4 - - + +
515B LYS* 4.4 12.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 629 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A LEU* 3.7 20.6 - - - -
593A LEU* 4.2 8.1 - - + +
599A ILE* 4.1 20.4 - - - -
603A MET* 4.1 11.2 - - - -
607A ILE* 4.0 16.6 - - - -
625A ASN 3.0 17.2 + - - -
626A LEU* 3.2 7.4 + - - +
628A LEU* 1.3 76.2 - - - +
630A CYS* 1.3 59.9 + - - +
631A LEU 3.2 0.7 - - - -
632A LEU* 3.0 24.0 + - - +
633A ASP 3.2 10.4 + - - -
636A LEU* 3.9 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 630 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A LEU* 2.9 42.4 + - - -
627A GLY* 3.0 8.9 + - - +
629A CYS* 1.3 77.8 - - - +
631A LEU* 1.3 61.1 + - - +
633A ASP 3.0 22.6 - - - +
636A LEU* 4.0 11.0 - - - -
637A ALA* 3.8 24.0 - - + +
640A ASN* 4.3 7.2 - - - -
644A LEU* 5.4 1.1 - - - -
666A ILE* 3.9 26.5 - - + -
670A HIS* 3.1 13.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 631 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A GLY 3.1 11.4 + - - +
628A LEU* 3.9 10.8 - - - +
629A CYS 3.2 0.6 - - - -
630A CYS* 1.3 75.6 - - - +
632A LEU* 1.3 66.8 + - + +
665A ASP* 3.5 36.8 - - + +
666A ILE* 3.7 13.5 - - + +
669A VAL* 3.8 23.6 - - + +
670A HIS* 3.6 16.2 + - - +
512B LEU* 4.3 14.4 - - + -
514B ILE* 4.2 22.9 - - + -
515B LYS* 4.1 26.7 - - + +
518B GLN* 4.8 2.5 - - - +
----------------------------------------------------------
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