Contacts of the helix formed by residues 608 - 622 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581F TRP* 3.8 4.5 - - - -
604F ASP* 4.4 7.4 + - - -
606F GLU 4.3 0.2 - - - -
607F PHE* 1.3 77.6 - - - +
609F LEU* 1.3 72.0 - - - +
610F SER* 2.9 27.1 + - - -
611F VAL* 3.7 13.1 - - - +
612F TYR* 3.6 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 609 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581F TRP* 4.6 22.0 - - + +
604F ASP* 4.4 15.9 - - - +
608F SER* 1.3 81.5 - - - +
610F SER* 1.3 63.3 + - - +
612F TYR* 4.0 1.6 - - + -
613F GLN* 2.7 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 610 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608F SER* 2.9 16.3 + - - -
609F LEU* 1.3 76.1 - - - +
611F VAL* 1.3 73.1 + - - +
612F TYR 3.1 1.1 - - - -
613F GLN* 3.5 3.3 + - - +
614F LYS* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 611 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385F GLU* 5.9 0.9 - - - +
606F GLU 5.5 1.6 - - - +
607F PHE* 3.5 34.8 - - + -
608F SER* 3.7 23.2 + - - +
609F LEU 3.6 0.2 - - - -
610F SER* 1.3 85.3 + - - +
612F TYR* 1.3 60.4 + - - +
614F LYS* 3.6 9.0 - - + +
615F MET* 3.2 25.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 612 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388F MET* 4.0 18.2 - - + -
391F VAL* 3.3 27.7 + - + +
392F ALA* 4.4 4.4 + - + -
581F TRP* 3.4 53.4 - + + -
582F TYR* 2.8 43.4 + + - -
607F PHE* 5.0 1.3 - - + -
608F SER 3.6 9.7 + - - +
609F LEU* 3.9 1.3 - - + +
610F SER 3.1 0.4 - - - -
611F VAL* 1.3 74.9 - - - +
613F GLN* 1.3 86.2 + - - +
614F LYS 3.0 3.6 - - - -
615F MET* 2.8 46.0 + - + +
616F LYS* 3.4 21.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 613 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156 PHE 5.3 9.4 - - - +
582F TYR* 5.1 1.2 + - - -
609F LEU* 2.7 42.8 + - - +
610F SER* 4.3 2.2 - - - +
612F TYR* 1.3 99.8 - - - +
614F LYS* 1.3 56.8 + - - +
615F MET 3.1 0.2 - - - -
616F LYS* 3.3 20.8 + - + +
617F PHE* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 614 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610F SER 3.0 19.3 + - - +
611F VAL* 3.6 13.0 - - + +
612F TYR 3.0 0.2 - - - -
613F GLN* 1.3 78.3 - - - +
615F MET* 1.3 58.6 + - + +
617F PHE* 3.2 41.1 - - + +
618F ASN* 2.8 23.6 + - - -
627F ASP* 4.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 615 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385F GLU 4.4 1.6 - - - +
388F MET* 3.8 20.9 - - + +
389F ALA* 3.7 14.4 - - - -
392F ALA* 4.1 10.5 - - + -
607F PHE* 4.2 16.6 - - + -
611F VAL* 3.2 13.0 - - + +
612F TYR* 2.8 46.9 + - + +
614F LYS* 1.3 76.0 - - + +
616F LYS* 1.3 61.5 + - - +
617F PHE 3.0 5.2 + - - -
618F ASN* 3.2 11.3 + - - +
619F VAL* 3.1 18.5 + - - +
625F VAL* 3.2 27.0 - - + +
626F LEU* 3.6 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 616 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146 ILE 3.1 20.9 + - - -
156 PHE* 3.7 20.0 - - + +
392F ALA* 3.5 19.7 - - + +
395F HIS* 2.9 42.0 + - - -
396F CYS* 4.1 11.7 - - - -
582F TYR* 3.3 13.9 + - - -
612F TYR* 3.8 32.1 - - + +
613F GLN* 3.3 20.8 + - + +
615F MET* 1.3 75.8 - - - +
617F PHE* 1.3 60.6 + - - +
619F VAL* 3.1 24.6 - - - +
620F ALA 3.2 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 617 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156 PHE* 5.7 1.1 - - - -
466 ILE* 4.4 10.3 - - + -
496 CYS* 5.4 3.6 - - + -
506 THR* 3.0 39.9 - - + -
556 VAL* 6.3 4.0 - - + -
613F GLN 2.9 13.8 + - - +
614F LYS* 3.2 33.9 - - + +
615F MET 3.0 0.2 - - - -
616F LYS* 1.3 74.5 - - - +
618F ASN* 1.3 76.0 + - - +
619F VAL 3.0 1.8 - - - -
620F ALA* 2.9 24.0 + - + +
621F MET* 3.1 40.8 + - + +
623F ILE* 5.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 618 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614F LYS* 2.8 24.4 + - - +
615F MET 3.2 5.1 + - - +
617F PHE* 1.3 87.4 - - - +
619F VAL* 1.3 57.3 + - - +
621F MET* 3.2 3.9 + - - +
622F GLY 2.8 24.8 + - - -
623F ILE* 3.0 39.2 + - + +
624F GLY 3.1 23.6 + - - +
625F VAL 3.2 19.4 + - - -
627F ASP* 3.3 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 619 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392F ALA* 4.6 0.2 - - + -
393F TRP* 4.4 10.5 - - + +
396F CYS* 3.6 31.9 - - + -
552F TYR* 3.1 41.8 - - + +
553F LEU* 4.1 8.7 - - + -
556F CYS* 4.0 15.3 - - + -
615F MET 3.1 17.5 - - - +
616F LYS* 3.1 17.0 - - - +
617F PHE 3.0 0.4 - - - -
618F ASN* 1.3 76.8 - - - +
620F ALA* 1.3 65.5 + - - +
621F MET 3.3 0.3 + - - -
622F GLY 3.5 1.2 + - - -
625F VAL* 3.5 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 620 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156 PHE* 3.8 27.1 - - + -
436 GLY* 4.1 18.7 - - - +
466 ILE* 3.4 33.4 - - + +
552F TYR* 3.8 11.8 - - - +
616F LYS 3.2 2.7 + - - +
617F PHE* 2.9 11.8 + - + +
619F VAL* 1.3 81.5 - - - +
621F MET* 1.3 72.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 621 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436 GLY* 5.0 4.6 - - - +
466 ILE* 3.2 48.2 - - + +
476 ALA* 4.3 12.5 - - + +
506 THR* 3.6 22.2 - - - -
552F TYR* 4.8 2.6 - - - +
555F HIS* 5.6 2.1 - - - -
617F PHE* 3.1 35.8 + - + +
618F ASN* 3.4 12.8 - - - +
619F VAL 3.1 0.2 - - - -
620F ALA* 1.3 82.6 - - + +
622F GLY* 1.3 58.4 + - - +
623F ILE* 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 622 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552F TYR* 3.9 16.6 - - - -
555F HIS* 2.8 32.7 - - - +
556F CYS 4.0 0.2 - - - -
559F ARG* 2.8 29.5 + - - -
618F ASN 2.8 8.1 + - - -
619F VAL 3.5 1.6 + - - -
621F MET* 1.3 75.8 - - - +
623F ILE* 1.3 58.4 + - - +
----------------------------------------------------------
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