Contacts of the helix formed by residues 608 - 622 (chain E) in PDB entry 4E2I
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 SER 608 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581E TRP* 3.8 4.9 - - - -
604E ASP* 4.4 7.4 + - - -
607E PHE* 1.3 77.8 - - - +
609E LEU* 1.3 72.1 + - - +
610E SER* 2.9 27.2 + - - -
611E VAL* 3.7 12.9 - - - +
612E TYR* 3.6 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 609 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581E TRP* 4.5 22.2 - - + +
604E ASP* 4.4 16.2 - - - +
608E SER* 1.3 82.3 - - - +
610E SER* 1.3 63.6 + - - +
612E TYR* 4.0 1.3 - - + -
613E GLN* 2.7 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 610 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608E SER* 2.9 15.6 + - - -
609E LEU* 1.3 75.6 - - - +
611E VAL* 1.3 73.4 + - - +
612E TYR 3.1 1.3 - - - -
613E GLN* 3.5 2.9 + - - +
614E LYS* 3.0 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 611 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385E GLU* 5.9 0.9 - - - +
606E GLU 5.5 1.8 - - - +
607E PHE* 3.5 34.3 - - + -
608E SER* 3.7 22.6 + - - +
610E SER* 1.3 86.3 + - - +
612E TYR* 1.3 60.0 + - - +
614E LYS* 3.6 9.4 - - + +
615E MET* 3.2 24.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 612 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388E MET* 4.0 18.8 - - + -
391E VAL* 3.3 27.3 + - + +
392E ALA* 4.7 4.7 - - + -
581E TRP* 3.4 54.3 - + + -
582E TYR* 2.8 43.7 + + - -
607E PHE* 5.0 1.2 - - + -
608E SER 3.6 9.5 + - - +
609E LEU* 3.9 0.9 - - + +
610E SER 3.1 0.8 - - - -
611E VAL* 1.3 74.5 - - - +
613E GLN* 1.3 84.1 + - - +
614E LYS 3.0 3.8 - - - -
615E MET* 2.9 47.3 + - + +
616E LYS* 3.4 19.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 613 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155 PHE 6.1 0.7 - - - +
582E TYR* 5.1 1.2 + - - -
609E LEU* 2.7 44.3 + - - +
610E SER* 4.3 2.2 - - - +
612E TYR* 1.3 98.4 - - - +
614E LYS* 1.3 57.4 + - - +
615E MET 3.1 0.2 - - - -
616E LYS* 3.3 21.3 + - + +
617E PHE* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 614 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505 THR* 5.1 11.2 - - + -
610E SER 3.0 20.4 + - - +
611E VAL* 3.6 13.0 - - + +
612E TYR 3.0 0.4 - - - -
613E GLN* 1.3 78.4 - - - +
615E MET* 1.3 59.7 + - + +
617E PHE* 3.3 38.6 - - + +
618E ASN* 2.8 24.0 + - - -
627E ASP* 4.0 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 615 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385E GLU 4.4 1.6 - - - +
388E MET* 3.8 20.6 - - + +
389E ALA* 3.7 14.4 - - - -
392E ALA* 4.1 9.6 - - + -
607E PHE* 4.2 16.6 - - + -
611E VAL* 3.2 13.2 - - + +
612E TYR* 2.9 46.5 + - + +
614E LYS* 1.3 77.3 - - + +
616E LYS* 1.3 61.6 - - - +
617E PHE 3.0 5.5 + - - -
618E ASN* 3.2 12.1 + - - +
619E VAL* 3.1 17.3 + - - +
625E VAL* 3.2 26.5 - - + +
626E LEU* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 616 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145 ILE 4.3 8.0 + - - -
155 PHE* 4.1 19.9 - - + +
392E ALA* 3.5 19.7 - - + -
395E HIS* 2.9 46.6 + - - -
396E CYS* 4.1 15.0 - - - -
582E TYR* 3.3 13.3 + - - +
612E TYR* 3.8 32.8 - - + +
613E GLN* 3.3 20.6 + - + +
615E MET* 1.3 75.2 - - - +
617E PHE* 1.3 61.2 + - - +
619E VAL* 3.1 26.0 - - - +
620E ALA 3.2 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 617 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155 PHE* 6.1 0.2 - - - -
465 ILE* 3.0 41.7 - - + -
475 ALA* 3.8 7.4 - - + -
505 THR* 3.1 30.3 - - + -
613E GLN 2.9 13.2 + - - +
614E LYS* 3.3 31.2 - - + +
616E LYS* 1.3 74.7 - - - +
618E ASN* 1.3 75.0 + - - +
619E VAL 3.0 1.3 - - - -
620E ALA* 2.9 24.4 + - - +
621E MET* 3.1 45.1 + - + +
623E ILE* 5.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 618 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614E LYS* 2.8 25.0 + - - +
615E MET 3.2 5.2 + - - +
617E PHE* 1.3 87.9 - - - +
619E VAL* 1.3 56.8 + - - +
621E MET* 3.4 3.5 - - - +
622E GLY 2.9 25.5 + - - -
623E ILE* 3.0 39.3 + - + +
624E GLY 3.1 24.5 + - - +
625E VAL 3.2 19.4 + - - -
627E ASP* 3.3 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 619 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392E ALA* 4.6 0.2 - - + -
393E TRP* 4.3 9.9 - - + +
396E CYS* 3.6 32.1 - - + -
552E TYR* 3.1 41.1 - - + +
553E LEU* 4.1 8.7 - - + -
556E CYS* 4.0 16.2 - - + -
615E MET 3.1 18.4 - - - +
616E LYS* 3.1 16.2 - - - +
617E PHE 3.0 0.4 - - - -
618E ASN* 1.3 77.3 - - - +
620E ALA* 1.3 65.2 + - - +
621E MET 3.3 0.3 + - - -
622E GLY 3.5 1.4 + - - -
625E VAL* 3.5 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 620 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155 PHE* 3.5 33.1 - - + -
395 GLU 5.3 0.5 - - - +
435 GLY* 3.4 18.0 - - - -
465 ILE* 3.6 17.0 - - + -
552E TYR* 3.8 13.3 - - - +
616E LYS 3.2 3.4 + - - +
617E PHE* 2.9 12.9 + - - +
619E VAL* 1.3 80.5 - - - +
621E MET* 1.3 76.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 621 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435 GLY* 3.0 31.7 - - - +
445 GLU* 5.3 4.6 - - - +
465 ILE* 3.8 10.8 - - + -
475 ALA* 3.4 22.7 - - - +
552E TYR* 4.8 2.7 - - - +
555E HIS* 5.6 2.3 - - - -
617E PHE* 3.1 48.4 + - + +
618E ASN* 3.4 12.3 - - - +
619E VAL 3.1 0.2 - - - -
620E ALA* 1.3 91.8 - - + +
622E GLY* 1.3 59.2 + - - +
623E ILE* 3.7 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 622 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552E TYR* 3.9 16.6 - - - -
555E HIS* 2.8 34.0 - - - +
556E CYS* 4.6 0.2 - - - -
559E ARG* 2.8 29.1 + - - -
618E ASN 2.9 7.7 + - - -
619E VAL 3.5 1.4 + - - -
621E MET* 1.3 75.1 - - - +
623E ILE* 1.3 59.5 + - - +
----------------------------------------------------------
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