Contacts of the helix formed by residues 608 - 622 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581C TRP* 3.8 4.6 - - - -
604C ASP* 4.4 6.9 + - - -
606C GLU 4.4 0.2 + - - -
607C PHE* 1.3 77.6 - - - +
609C LEU* 1.3 71.7 + - - +
610C SER* 2.9 27.5 + - - -
611C VAL* 3.7 12.9 - - - +
612C TYR* 3.6 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 609 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581C TRP* 4.6 22.2 - - + +
604C ASP* 4.4 15.0 - - - +
608C SER* 1.3 82.1 - - - +
610C SER* 1.3 62.8 + - - +
612C TYR* 4.0 1.6 - - + -
613C GLN* 2.7 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 610 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608C SER* 2.9 15.2 + - - -
609C LEU* 1.3 76.7 - - - +
611C VAL* 1.3 73.2 + - - +
612C TYR 3.1 1.3 - - - -
613C GLN* 3.5 3.0 + - - +
614C LYS* 3.0 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 611 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C GLU* 5.9 1.3 - - - +
606C GLU 5.5 1.8 - - - +
607C PHE* 3.5 33.4 - - + -
608C SER* 3.7 22.1 + - - +
610C SER* 1.3 86.3 + - - +
612C TYR* 1.3 61.1 + - - +
614C LYS* 3.6 9.0 - - + +
615C MET* 3.2 25.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 612 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C MET* 4.0 18.6 - - + -
391C VAL* 3.3 26.1 + - + +
392C ALA* 4.7 4.0 - - + -
581C TRP* 3.4 52.3 - + + -
582C TYR* 2.8 43.4 + + - -
607C PHE* 5.1 0.8 - - - -
608C SER 3.6 9.1 + - - +
609C LEU* 3.9 0.9 - - + +
610C SER 3.1 0.4 - - - -
611C VAL* 1.3 76.0 - - - +
613C GLN* 1.3 85.9 + - - +
614C LYS 3.0 3.8 - - - -
615C MET* 2.9 46.6 + - + +
616C LYS* 3.4 21.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 613 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582C TYR* 5.1 1.0 + - - -
609C LEU* 2.7 43.9 + - - +
610C SER* 4.3 2.0 - - - +
612C TYR* 1.3 98.9 - - - +
614C LYS* 1.3 57.0 + - - +
615C MET 3.1 0.2 - - - -
616C LYS* 3.3 20.5 + - + +
617C PHE* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 614 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503 THR* 5.3 8.3 - - + -
610C SER 3.0 19.8 + - - +
611C VAL* 3.6 12.1 - - + +
612C TYR 3.0 0.4 - - - -
613C GLN* 1.3 77.7 - - - +
615C MET* 1.3 58.8 + - + +
617C PHE* 3.2 40.7 - - + +
618C ASN* 2.8 23.6 + - - -
627C ASP* 4.0 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 615 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C GLU 4.4 1.8 - - - +
388C MET* 3.8 21.5 - - + +
389C ALA* 3.7 14.6 - - - -
392C ALA* 4.1 10.8 - - + -
607C PHE* 4.2 17.7 - - + -
611C VAL* 3.2 13.5 - - + +
612C TYR* 2.9 44.7 + - + +
614C LYS* 1.3 77.1 - - + +
616C LYS* 1.3 61.6 + - - +
617C PHE 3.0 5.2 + - - -
618C ASN* 3.2 11.6 + - - +
619C VAL* 3.1 17.1 + - - +
625C VAL* 3.2 26.4 - - + +
626C LEU* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 616 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143 ILE 4.6 7.6 + - - -
153 PHE* 4.4 12.4 - - + +
392C ALA* 3.5 19.1 - - + -
395C HIS* 2.9 45.1 + - - -
396C CYS* 4.1 18.7 - - - -
582C TYR* 3.3 13.3 + - - -
612C TYR* 3.8 33.4 - - + +
613C GLN* 3.3 20.6 + - + +
615C MET* 1.3 76.7 - - - +
617C PHE* 1.3 60.7 + - - +
619C VAL* 3.1 25.5 - - - +
620C ALA* 3.2 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 617 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153 PHE* 6.3 0.2 - - - -
463 ILE* 3.2 29.8 - - + -
473 ALA* 4.2 2.5 - - - -
503 THR* 2.8 44.9 - - + -
613C GLN 2.9 13.6 + - - +
614C LYS* 3.2 32.1 - - + +
616C LYS* 1.3 74.1 - - - +
618C ASN* 1.3 72.6 + - - +
619C VAL 3.0 3.8 - - - -
620C ALA* 2.9 25.2 + - - +
621C MET* 3.1 44.5 + - + +
623C ILE* 5.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 618 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614C LYS* 2.8 24.0 + - - +
615C MET 3.2 4.8 + - - +
617C PHE* 1.3 88.0 - - - +
619C VAL* 1.3 57.3 + - - +
621C MET* 3.2 4.8 + - - +
622C GLY 2.8 25.1 + - - -
623C ILE* 3.0 39.7 + - + +
624C GLY 3.1 24.0 + - - +
625C VAL* 3.2 20.0 + - - -
627C ASP* 3.3 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 619 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C TRP* 4.3 10.5 - - + +
396C CYS* 3.6 31.4 - - + -
552C TYR* 3.1 41.1 - - + +
553C LEU* 4.1 9.2 - - + -
556C CYS* 4.0 15.7 - - + -
615C MET 3.1 18.6 - - - +
616C LYS* 3.1 16.4 - - - +
617C PHE 3.0 0.2 - - - -
618C ASN* 1.3 79.2 - - - +
620C ALA* 1.3 62.3 + - - +
621C MET 3.3 0.3 + - - -
622C GLY 3.5 1.4 + - - -
625C VAL* 3.5 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 620 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153 PHE* 3.7 32.5 - - + -
433 GLY* 3.5 19.9 - - - -
463 ILE* 3.8 15.9 - - + -
552C TYR* 3.8 13.7 - - - +
616C LYS 3.2 4.0 + - - +
617C PHE* 2.9 12.9 + - - +
619C VAL* 1.3 79.3 - - - +
621C MET* 1.3 76.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 621 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433 GLY* 3.3 22.8 - - - +
443 GLU* 5.1 5.4 - - - +
463 ILE* 3.8 12.8 - - + -
473 ALA* 3.3 29.4 - - - +
552C TYR* 4.8 2.8 - - - +
555C HIS* 5.6 1.9 - - - -
617C PHE* 3.1 51.1 + - + +
618C ASN* 3.4 12.1 - - - +
619C VAL 3.1 0.2 - - - -
620C ALA* 1.3 91.4 - - + +
622C GLY* 1.3 59.6 + - - +
623C ILE* 3.7 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 622 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552C TYR* 3.9 16.4 - - - -
555C HIS* 2.9 33.7 - - - +
559C ARG* 2.8 29.5 + - - -
618C ASN 2.8 8.1 + - - -
619C VAL 3.5 1.4 + - - -
621C MET* 1.3 75.7 - - - +
623C ILE* 1.3 58.2 + - - +
----------------------------------------------------------
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