Contacts of the helix formed by residues 609 - 627 (chain A) in PDB entry 1F9O
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 ARG 609 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A HIS* 3.4 15.3 - - - +
37A SER* 3.9 5.8 - - - -
42A MET* 4.5 4.2 - - + +
44A GLU* 3.1 40.5 + - - +
494A ASP* 5.4 4.8 + - - -
542A GLU* 2.9 42.0 + - - -
544A ARG* 3.7 4.0 - - - +
607A LEU* 3.6 27.2 + - + +
608A HIS* 1.3 71.8 - - - +
610A PHE* 1.3 66.0 + - - +
611A TRP* 4.2 16.8 - - + +
612A ALA* 2.9 28.4 + - + +
613A GLN* 3.1 16.0 + - - +
1C V3P 4.4 0.2 + - - -
2C BGC 3.4 27.6 - - - -
3C BGC 4.2 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 3.7 26.0 - - + -
27A TYR* 4.1 30.1 - + + -
28A PHE* 3.9 17.3 - + - -
34A PRO* 3.8 23.3 - - + -
35A TYR 3.1 23.8 - - - +
36A HIS* 3.0 11.0 + - - +
37A SER* 4.2 0.6 - - - +
56A ALA* 3.5 33.7 - - + -
59A TYR* 4.3 1.6 - - + -
60A TYR* 3.9 22.2 - + + -
63A LEU* 4.8 1.8 - - + -
608A HIS 3.5 3.4 + - - -
609A ARG* 1.3 71.6 - - - +
611A TRP* 1.3 66.5 + - - +
613A GLN* 3.3 3.4 + - + +
614A SER* 3.1 44.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A HIS* 4.3 9.6 - + - -
55A GLU* 3.6 20.4 - - + +
56A ALA* 5.4 3.6 - - + +
59A TYR* 3.7 35.3 - - + -
411A TRP* 4.1 15.7 - + - -
417A TRP* 3.4 42.6 - + - -
494A ASP* 4.6 0.4 - - - -
496A GLY* 3.8 33.0 - - - -
497A CYS* 4.3 2.7 - - - -
609A ARG* 4.2 18.0 - - + +
610A PHE* 1.3 83.3 - - + +
612A ALA* 1.3 61.2 + - + +
614A SER 3.8 0.4 - - - +
615A GLU* 2.9 42.6 + - + +
2C BGC 3.8 22.0 - - - -
3C BGC 2.9 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A ASP* 5.5 0.7 - - - +
495A LEU* 4.8 4.5 - - + -
496A GLY* 3.7 28.8 - - - +
499A SER* 4.5 0.9 + - - -
538A ILE* 4.9 2.7 - - + +
609A ARG* 2.9 25.0 + - + +
611A TRP* 1.3 89.9 - - + +
613A GLN* 1.3 73.1 + - - +
615A GLU* 3.3 3.0 + - - +
616A PHE* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A MET* 3.3 17.7 - - + +
20A ILE* 3.8 20.9 - - + -
27A TYR* 3.2 29.1 + - + +
495A LEU* 5.9 0.6 - - - +
537A GLY* 3.4 10.7 - - - -
538A ILE* 3.1 49.6 + - - +
607A LEU 4.5 1.6 + - - -
608A HIS* 3.9 18.2 - - - +
609A ARG 3.1 15.7 + - - +
610A PHE* 3.6 5.2 - - - +
612A ALA* 1.3 80.8 - - - +
614A SER* 1.3 62.1 + - - +
616A PHE* 3.0 4.1 + - - -
617A ALA* 3.0 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 3.8 12.8 - - - +
59A TYR* 3.9 28.7 + - - -
63A LEU* 4.2 13.3 - - - +
610A PHE* 3.1 40.5 + - - -
611A TRP 4.0 2.9 - - - -
613A GLN* 1.3 76.0 - - - +
615A GLU* 1.3 57.8 + - - +
617A ALA* 3.2 0.9 + - - +
618A VAL* 2.8 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 2.6 38.9 + - + -
62A TRP* 3.9 15.8 - - - -
417A TRP* 3.1 16.7 + - - -
420A GLN* 5.8 0.9 - - - +
496A GLY 3.5 8.5 - - - +
499A SER* 3.6 2.5 - - - -
500A SER* 3.5 39.0 + - - +
503A ASN* 4.5 7.1 + - - -
611A TRP* 2.9 21.5 + - + +
612A ALA* 3.4 9.6 - - - +
613A GLN 3.2 0.2 - - - -
614A SER* 1.3 79.1 - - - +
616A PHE* 1.3 56.7 + - - +
618A VAL* 4.0 3.9 - - - +
619A ALA* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 616 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A MET* 3.6 32.5 - - + -
499A SER* 3.4 23.3 - - - +
525A LEU* 4.1 16.2 - - + -
528A MET* 3.7 30.5 - - + -
529A TRP* 3.9 37.0 - + + -
538A ILE* 3.5 35.4 - - + -
612A ALA 3.0 8.7 + - - +
613A GLN 3.0 7.8 + - - +
615A GLU* 1.3 74.9 - - - +
617A ALA* 1.3 62.7 + - - +
619A ALA* 3.5 2.0 + - - +
620A ASN* 2.8 48.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 617 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 3.3 28.8 - - + +
16A MET* 3.9 23.1 - - + -
17A TYR 5.0 0.7 - - - +
20A ILE* 4.6 0.9 - - + -
63A LEU* 3.8 14.8 - - + -
613A GLN 3.0 11.4 + - - +
614A SER 3.2 6.3 + - - +
616A PHE* 1.3 74.8 - - - +
618A VAL* 1.3 66.4 + - - +
620A ASN* 2.7 22.0 + - - +
621A GLY 2.9 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 618 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 4.1 3.3 - - - -
59A TYR* 5.7 0.2 - - + -
62A TRP* 3.7 55.0 - - + +
63A LEU* 4.2 21.1 - - + +
66A MET* 3.4 19.1 - - + +
503A ASN* 3.8 16.4 - - - +
614A SER* 2.8 27.5 + - - +
615A GLU* 4.0 5.2 - - - +
617A ALA* 1.3 72.2 - - - +
619A ALA* 1.3 63.7 + - - +
621A GLY* 2.9 2.9 + - - -
622A VAL* 2.9 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 619 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A SER* 3.7 21.5 - - - +
502A ALA* 4.6 0.8 - - + -
503A ASN* 4.4 18.8 - - + +
506A THR* 5.3 1.6 + - - -
525A LEU* 3.8 20.5 - - + +
615A GLU 3.0 21.0 + - - +
616A PHE* 3.5 7.4 - - - +
617A ALA 3.1 0.2 - - - -
618A VAL* 1.3 76.1 - - - +
620A ASN* 1.3 62.8 + - - +
622A VAL* 3.3 5.1 + - - +
623A TYR* 3.2 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 620 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 3.8 37.9 - - - +
12A ARG* 4.1 21.1 + - - +
13A PHE 4.2 7.0 - - - +
525A LEU* 3.7 21.1 - - - +
616A PHE* 2.8 55.8 + - - -
617A ALA* 2.7 15.1 + - - +
619A ALA* 1.3 73.2 - - - +
621A GLY* 1.3 60.8 + - - +
623A TYR* 3.4 3.2 + - - +
624A ALA* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 621 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 4.4 3.5 - - - +
66A MET* 3.7 24.5 - - - -
70A PHE* 3.9 15.0 - - - -
617A ALA 2.9 7.7 + - - -
618A VAL 2.9 7.3 + - - -
620A ASN* 1.3 78.8 - - - +
622A VAL* 1.3 61.8 + - - +
624A ALA* 3.3 3.4 + - - +
625A ILE* 3.1 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 622 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TRP* 5.8 1.6 - - + +
66A MET* 3.8 11.4 - - + +
503A ASN* 3.8 24.0 - - - +
506A THR* 3.9 19.3 - - + -
507A TYR* 3.5 44.0 - - + +
618A VAL* 2.9 21.5 + - + +
619A ALA* 3.7 7.6 - - - +
620A ASN 3.3 0.2 - - - -
621A GLY* 1.3 75.4 - - - +
623A TYR* 1.3 63.8 + - - +
625A ILE* 3.3 5.8 + - - +
626A LEU* 3.0 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 623 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASN* 4.7 2.5 - - - -
9A TYR* 3.5 39.9 - + + -
506A THR* 3.8 28.0 - - + +
518A ARG* 2.7 42.9 + - + +
521A ALA* 5.0 0.9 - - + -
522A GLN* 3.7 28.5 + - + +
525A LEU* 3.8 19.7 - - + -
619A ALA 3.2 10.8 + - - +
620A ASN* 3.7 7.4 - - - +
622A VAL* 1.3 77.5 - - - +
624A ALA* 1.3 65.6 + - - +
627A PHE* 3.0 56.9 + + + +
629A ASP 5.5 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 624 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ALA* 3.2 7.1 - - + +
6A ASN* 2.8 55.7 + - - +
9A TYR* 3.8 3.8 - - + +
10A GLN* 3.7 19.3 - - + +
70A PHE* 4.3 9.6 - - + -
620A ASN 3.1 17.0 + - - +
621A GLY 3.6 4.5 - - - +
623A TYR* 1.3 77.1 - - - +
625A ILE* 1.3 60.8 + - - +
628A PRO* 4.1 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 625 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 5.4 7.2 + - - +
4A PRO 4.8 2.1 - - - +
5A ALA* 4.4 3.6 - - - -
66A MET* 4.4 5.8 - - + -
69A ARG* 3.7 47.6 - - + +
70A PHE* 4.1 12.1 - - + -
245A TRP* 4.2 23.8 - - + +
427A TYR* 5.9 0.2 - - - +
621A GLY 3.1 21.1 + - - +
622A VAL* 3.7 5.4 - - - +
623A TYR 3.1 0.2 - - - -
624A ALA* 1.3 79.4 - - - +
626A LEU* 1.3 76.9 + - + +
628A PRO* 3.7 13.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
427A TYR* 3.6 33.2 - - + +
506A THR* 3.8 10.5 - - + +
507A TYR* 3.7 37.9 - - + -
510A ALA* 3.5 27.7 - - + +
622A VAL* 3.0 18.7 + - + +
625A ILE* 1.3 90.9 - - + +
627A PHE* 1.3 78.5 + - + +
628A PRO* 3.4 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 627 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASN* 3.0 26.7 + - - +
506A THR* 3.7 30.5 - - + -
509A ALA* 4.2 5.8 - - + -
510A ALA* 3.7 27.8 - - + -
518A ARG* 3.5 36.8 - - + -
623A TYR* 3.0 44.9 + + + +
624A ALA 4.2 0.7 - - - -
626A LEU* 1.3 91.9 - - + +
628A PRO* 1.3 56.7 - - - +
629A ASP 3.0 13.2 + - - +
----------------------------------------------------------
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