Contacts of the helix formed by residues 612 - 626 (chain A) in PDB entry 1GGE
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 612 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A GLU 3.4 2.5 + - - -
611A VAL* 1.3 73.9 - - - +
613A SER* 1.3 63.7 + - - +
614A ALA* 3.1 15.4 - - + +
615A ASP* 2.9 45.7 + - - +
616A LEU 3.3 8.0 + - - -
643A ASP* 3.2 15.3 - - - +
669A CYS* 3.0 43.9 + - + +
670A GLY* 4.2 3.8 - - - +
699A GLY* 3.9 3.8 - - - +
722A ASP 3.0 23.4 + - - -
723A SER* 3.2 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A VAL* 3.0 3.9 + - - -
612A ARG* 1.3 70.7 - - - +
614A ALA* 1.3 58.7 + - - +
616A LEU* 3.3 9.7 + - - +
617A LEU* 2.8 31.8 + - - +
642A ALA* 4.2 9.0 - - - -
643A ASP* 2.7 27.4 + - - -
644A ASP* 3.4 35.0 + - - +
646A THR* 5.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ARG* 3.1 15.8 - - + +
613A SER* 1.3 81.6 + - - +
615A ASP* 1.3 65.3 + - - +
617A LEU* 3.7 10.2 - - - +
618A ALA* 3.3 21.0 + - - +
643A ASP* 5.0 0.2 + - - -
724A ALA 4.5 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ARG* 2.9 48.5 + - - +
614A ALA* 1.3 78.7 - - - +
616A LEU* 1.3 57.6 + - - +
618A ALA* 3.2 4.3 + - - +
619A ILE* 2.9 33.0 + - - +
668A PRO* 4.0 14.4 - - + -
669A CYS 2.9 21.2 + - - -
698A ALA* 3.7 3.8 - - - +
723A SER* 3.5 3.6 - - - -
724A ALA* 2.8 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 616 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A ILE* 4.2 31.4 - - + -
607A LEU* 5.0 4.0 - - + -
611A VAL* 4.2 12.3 - - + -
612A ARG 3.3 7.6 + - - +
613A SER* 3.3 10.6 + - - +
615A ASP* 1.3 78.4 - - - +
617A LEU* 1.3 63.5 + - - +
619A ILE* 3.2 7.2 + - + +
620A LEU* 2.9 56.0 + - + +
632A LEU* 4.5 8.7 - - + -
642A ALA* 5.7 2.0 - - + -
646A THR* 5.9 1.3 - - + -
648A LEU* 3.7 41.5 - - + -
668A PRO* 4.9 2.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 617 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A SER 2.8 21.0 + - - +
614A ALA* 3.7 9.6 - - - +
615A ASP 3.3 0.2 - - - -
616A LEU* 1.3 71.6 - - - +
618A ALA* 1.3 63.5 + - - +
620A LEU* 4.1 4.4 - - - +
621A LYS* 3.1 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 618 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A ALA 3.3 6.8 + - - +
615A ASP 3.2 4.8 + - - +
617A LEU* 1.3 76.9 - - - +
619A ILE* 1.3 67.8 + - - +
621A LYS* 3.9 7.9 - - - +
622A ALA* 3.2 22.5 + - - +
724A ALA 3.3 30.1 - - - +
725A ASP* 4.4 10.1 - - - -
729A MET* 3.9 3.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 619 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A ILE* 3.8 23.1 - - + -
615A ASP 2.9 28.2 + - - +
616A LEU* 3.6 9.4 - - + +
618A ALA* 1.3 76.9 - - - +
620A LEU* 1.3 63.9 + - + +
622A ALA 3.3 0.2 + - - -
623A LEU* 3.0 32.0 + - + +
666A ILE* 3.6 45.3 - - + -
668A PRO* 4.1 20.4 - - + -
724A ALA* 3.7 19.3 - - + -
729A MET* 3.7 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 620 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A ILE* 3.8 28.5 - - + -
616A LEU* 2.9 41.7 + - + +
617A LEU* 4.2 2.7 - - - +
619A ILE* 1.3 78.6 - - + +
621A LYS* 1.3 57.1 + - - +
623A LEU* 3.7 5.5 - - + +
624A LYS* 2.8 33.4 + - - +
630A ALA* 4.1 15.7 - - + -
632A LEU* 4.9 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 621 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A LEU* 3.1 23.1 + - + +
618A ALA* 3.9 7.0 - - - +
619A ILE 3.3 0.2 - - - -
620A LEU* 1.3 78.5 - - - +
622A ALA* 1.3 62.7 + - - +
624A LYS* 3.4 9.5 + - + +
625A ALA* 3.1 23.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 622 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ALA 3.2 11.5 + - - +
619A ILE 3.8 0.7 - - - +
621A LYS* 1.3 76.4 - - - +
623A LEU* 1.3 65.7 + - - +
625A ALA* 3.4 14.4 + - - +
626A LYS* 3.4 9.9 + - - +
726A GLY* 6.3 0.7 - - - -
729A MET* 3.4 35.7 - - + -
730A ASP* 6.2 0.2 - - - +
733A LEU* 3.7 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 623 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A VAL* 4.2 18.2 - - + -
605A ILE* 4.6 1.3 - - + -
619A ILE* 3.0 35.2 + - + +
620A LEU* 3.7 7.4 - - + +
622A ALA* 1.3 75.6 - - - +
624A LYS* 1.3 63.4 + - - +
626A LYS* 3.1 4.0 + - - -
627A GLY 3.0 4.0 + - - -
628A VAL* 2.9 55.7 + - + +
629A HIS 4.3 8.7 - - - +
630A ALA* 4.0 27.1 - - + -
666A ILE* 4.7 2.0 - - + -
729A MET* 3.6 19.5 - - + -
732A LEU* 4.8 1.3 - - + -
733A LEU* 4.2 13.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
620A LEU 2.8 18.6 + - - +
621A LYS* 3.7 8.3 - - + +
623A LEU* 1.3 77.7 - - - +
625A ALA* 1.3 61.5 + - - +
627A GLY* 3.2 13.4 + - - +
628A VAL 4.7 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 625 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A LYS* 3.1 17.2 + - + +
622A ALA* 3.7 8.1 - - - +
623A LEU 3.3 0.2 - - - -
624A LYS* 1.3 78.1 - - - +
626A LYS* 1.3 67.3 + - + +
627A GLY 3.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 626 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A VAL* 3.7 21.4 - - + +
599A LYS* 3.6 23.3 + - - +
622A ALA 3.4 10.9 + - - +
623A LEU 3.1 7.4 + - - +
625A ALA* 1.3 85.4 - - + +
627A GLY* 1.3 62.9 + - - +
628A VAL* 3.3 6.2 + - + -
730A ASP* 5.4 5.1 + - - -
733A LEU* 4.1 27.5 - - + +
----------------------------------------------------------
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