Contacts of the helix formed by residues 600 - 615 (chain H) in PDB entry 5G04
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 TYR 600 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507H ARG* 5.4 7.4 + - - -
534H GLU 5.4 0.2 + - - -
537H GLU* 2.6 49.0 + - + +
538H ILE* 6.1 0.5 - - - +
567H PRO* 3.6 25.4 - - + -
568H GLU* 4.1 7.4 + - - -
571H CYS* 5.3 0.2 - - - -
597H ASP* 3.4 29.8 - - + +
598H PRO 3.4 2.4 - - - -
599H ASN* 1.3 77.1 - - - +
601H ALA* 1.3 67.7 + - + +
602H TYR* 3.9 15.7 - - + +
603H ALA* 3.7 29.6 - - + +
604H TYR* 3.2 17.7 - - - -
630H VAL* 3.6 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 601 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600H TYR* 1.3 78.0 - - + +
602H TYR* 1.3 55.0 + - + +
604H TYR* 2.7 37.3 + - - +
605H THR* 3.5 6.0 + - - -
627H ALA* 4.3 4.6 - - - +
630H VAL* 3.5 17.2 - - + +
631H ASN* 3.8 33.0 - - + +
634H HIS* 4.1 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 602 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510H PHE* 4.0 8.4 - + - -
537H GLU* 4.1 19.5 - - + -
538H ILE* 3.7 24.9 - - + +
541H THR* 3.4 31.3 + - - +
571H CYS* 4.6 0.9 - - - -
600H TYR* 3.6 23.3 - - + +
601H ALA* 1.3 75.3 - - + +
603H ALA* 1.3 66.9 + - - +
605H THR* 3.1 11.4 - - + -
606H LEU* 3.0 54.9 + - + +
634H HIS* 3.3 22.4 - + + -
636H ASN* 3.6 22.0 - - + -
184L ARG 3.8 14.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 603 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571H CYS* 4.0 14.4 - - - -
590H PHE* 4.6 4.3 - - - +
593H ALA* 4.1 20.6 - - + -
594H ILE* 3.8 24.8 - - + +
600H TYR* 3.7 31.0 - - + +
602H TYR* 1.3 77.8 - - - +
604H TYR* 1.3 62.3 + - - +
606H LEU* 3.4 2.6 + - - +
607H LEU* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 604 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E LEU* 5.0 6.9 + - + +
103E LEU* 4.6 11.2 - - + -
594H ILE* 3.4 45.0 - - + +
597H ASP 4.7 0.2 - - - -
598H PRO* 2.7 37.9 + - + +
600H TYR 3.2 26.7 - - - -
601H ALA* 2.7 17.2 + - - +
603H ALA* 1.3 69.6 - - - +
605H THR* 1.3 54.1 + - - +
607H LEU* 3.0 5.6 + - - +
608H GLY* 2.6 32.7 + - - -
623H CYS* 3.9 16.4 - - + +
626H ASN* 3.6 33.2 - - + -
627H ALA* 3.8 15.0 - - + -
629H ARG* 4.0 13.3 + - - -
630H VAL* 3.9 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 605 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601H ALA 3.6 4.5 + - - -
602H TYR* 3.1 11.9 + - + -
604H TYR* 1.3 76.6 - - - +
606H LEU* 1.3 61.4 + - + +
608H GLY* 2.7 22.9 + - - -
609H HIS* 2.9 34.3 + - + +
624H PHE* 3.5 10.3 - - + -
627H ALA* 3.9 10.4 - - - +
634H HIS* 2.8 28.5 + - + -
636H ASN* 3.5 33.9 - - + -
637H ALA* 4.2 1.1 - - - +
184L ARG 4.1 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 606 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537H GLU 4.9 1.3 - - - +
541H THR* 4.0 2.0 - - - +
571H CYS* 3.7 11.4 - - - -
575H ASN* 3.7 25.6 - - - +
590H PHE* 3.5 33.9 - - + -
602H TYR* 3.0 45.5 + - + +
603H ALA 3.9 1.8 - - - +
605H THR* 1.3 81.3 - - + +
607H LEU* 1.3 63.6 + - - +
609H HIS* 3.4 11.8 + - + +
610H GLU* 3.2 25.1 + - - +
184L ARG* 4.0 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 607 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E LEU* 3.9 18.6 - - + -
587H ILE* 3.9 30.7 - - + +
590H PHE* 3.8 27.2 - - + -
591H GLN* 3.9 16.4 - - + -
594H ILE* 3.8 23.8 - - + -
603H ALA 3.0 12.9 + - - +
604H TYR 3.0 8.6 + - - +
606H LEU* 1.3 75.9 - - - +
608H GLY* 1.3 63.6 + - - +
610H GLU* 3.4 5.4 + - + +
611H PHE* 3.2 46.2 + - + -
623H CYS* 4.0 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 608 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604H TYR 2.6 17.1 + - - -
605H THR 2.7 8.8 + - - -
607H LEU* 1.3 70.6 - - - +
609H HIS* 1.3 55.7 + - - -
611H PHE* 3.0 21.4 + - - +
612H VAL* 3.1 13.9 + - - +
620H ALA* 3.7 2.7 - - - +
623H CYS* 3.9 16.7 - - - +
624H PHE* 3.5 22.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 609 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605H THR* 2.9 42.2 + - + +
606H LEU* 3.4 11.8 + - + +
608H GLY* 1.3 71.1 - - - +
610H GLU* 1.3 58.2 + - - +
612H VAL* 3.3 12.0 - - - +
613H LEU* 3.1 35.1 + - + +
624H PHE* 3.5 14.8 - + - -
636H ASN 4.1 4.6 + - - -
639H TYR* 3.8 31.6 - + - -
640H GLY* 4.6 0.2 - - - -
643H MET* 4.3 11.8 - - - +
182L SER* 5.3 2.3 + - - -
183L ILE 3.9 6.1 - - - -
184L ARG* 3.2 50.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 610 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578H SER* 2.7 32.8 + - - -
583H HIS* 3.0 38.8 - - - +
586H ALA* 4.1 2.6 - - + +
587H ILE* 3.8 21.5 - - + -
590H PHE* 3.7 29.5 - - + -
606H LEU 3.2 5.9 + - - +
607H LEU* 3.4 11.4 - - - +
609H HIS* 1.3 76.0 - - - +
611H PHE* 1.3 56.2 + - - +
613H LEU* 3.2 8.8 + - - +
614H THR* 2.6 36.5 + - - -
184L ARG* 3.5 14.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 611 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E ILE* 6.0 0.4 - - + -
103E LEU* 4.7 3.8 - - + -
587H ILE* 4.0 22.4 - - + -
591H GLN* 4.3 9.0 - - - -
607H LEU* 3.2 42.1 + - + -
608H GLY 3.0 3.1 + - - +
610H GLU* 1.3 74.2 - - - +
612H VAL* 1.3 65.4 + - - +
614H THR* 3.1 3.5 + - - -
615H GLU 2.9 4.9 + - - -
616H GLU* 2.9 58.2 + - + +
619H LYS* 3.5 27.1 - - + -
620H ALA* 3.2 25.6 - - + -
623H CYS* 3.4 32.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 612 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608H GLY 3.1 13.8 + - - +
609H HIS* 3.3 17.5 - - - +
611H PHE* 1.3 73.1 - - - +
613H LEU* 1.3 67.1 + - + +
615H GLU* 3.1 23.4 + - - +
617H LEU* 4.2 10.8 - - + +
620H ALA* 3.7 3.2 - - + +
624H PHE* 3.8 12.3 - - + -
640H GLY 5.2 0.9 - - - +
643H MET* 4.5 22.9 - - + -
644H ILE* 3.8 31.9 - - + +
647H LYS* 3.9 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 613 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544H TRP* 5.2 9.4 - - + -
578H SER* 4.7 4.5 - - - +
581H ARG* 5.9 1.6 - - + -
583H HIS* 3.6 35.1 - - + +
609H HIS* 3.1 24.6 + - + +
610H GLU* 3.2 24.4 + - - +
612H VAL* 1.3 81.5 - - + +
614H THR* 1.3 60.6 + - - +
615H GLU* 3.1 13.1 + - - +
643H MET* 6.2 1.8 - - + -
647H LYS* 5.4 3.6 - - - +
23L ARG* 4.8 6.1 - - - -
181L ARG* 6.4 0.2 - - - +
184L ARG* 4.6 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 614 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583H HIS* 3.8 22.2 + - + +
584H ASP* 5.5 8.7 - - - +
587H ILE* 3.7 16.2 - - + +
610H GLU 2.6 25.2 + - - -
611H PHE* 3.1 5.5 + - - -
613H LEU* 1.3 75.0 - - - +
615H GLU* 1.3 66.8 + - - +
616H GLU* 3.7 26.7 + - + +
23L ARG* 3.5 22.5 + - - +
27L SER* 6.2 0.2 - - - +
28L GLN* 5.4 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 615 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611H PHE 2.9 2.8 + - - -
612H VAL 3.1 14.3 + - - +
613H LEU 3.1 9.1 - - - +
614H THR* 1.3 80.8 - - - +
616H GLU* 1.3 57.8 + - - +
617H LEU* 3.3 21.8 + - + +
647H LYS* 5.4 6.1 - - + +
23L ARG* 2.9 35.8 + - - +
28L GLN* 3.5 21.0 + - - +
70L ARG* 4.6 20.0 + - - +
162L VAL* 5.5 1.2 - - - +
163L GLU* 4.3 26.1 + - - +
----------------------------------------------------------
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