Contacts of the helix formed by residues 592 - 607 (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 ILE 592 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362E THR* 4.1 12.6 - - + +
365E PHE* 3.7 33.0 - - + -
366E ASN* 3.4 31.6 - - - +
369E LEU* 4.5 4.0 - - + -
588E PHE* 3.6 12.6 - - + -
589E ALA* 3.0 41.1 + - + +
591E SER* 1.3 81.6 - - - +
593E GLN* 1.3 57.2 + - - +
594E SER 3.0 3.4 - - - -
595E ARG* 2.8 28.8 + - + +
596E ILE* 3.0 23.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 593 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585E VAL* 3.1 44.5 - - + +
586E ALA* 4.3 8.3 + - - +
588E PHE* 3.6 9.8 + - + +
589E ALA 2.9 18.5 + - - +
590E GLN* 3.1 40.8 + - - +
591E SER 3.7 0.2 - - - -
592E ILE* 1.3 79.0 - - - +
594E SER* 1.3 58.5 + - - +
596E ILE* 4.0 4.3 - - - -
597E VAL* 3.1 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 594 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590E GLN 5.0 3.3 + - - -
591E SER 5.5 4.3 - - - -
592E ILE 3.0 1.7 + - - +
593E GLN* 1.3 78.1 - - - +
595E ARG* 1.3 59.1 + - - +
597E VAL* 4.1 6.4 + - - +
598E GLU* 3.1 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 595 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366E ASN* 3.2 41.4 + - - +
369E LEU* 3.2 28.0 - - + +
370E ASP* 3.1 37.6 + - - +
373E ASP* 2.8 28.7 + - - -
592E ILE* 2.8 17.2 + - + +
594E SER* 1.3 79.8 - - - +
596E ILE* 1.3 63.7 + - - +
597E VAL 3.3 0.4 - - - -
598E GLU* 3.1 34.3 - - - +
599E TRP* 3.6 15.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 596 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365E PHE* 5.6 1.1 - - + -
369E LEU* 4.8 8.5 - - + -
576E LEU* 6.0 0.7 - - + -
580E ILE* 3.6 23.6 - - + +
585E VAL* 4.0 6.3 - - + -
588E PHE* 3.4 61.2 - - + -
592E ILE* 3.0 35.4 + - + +
593E GLN* 3.8 7.0 - - - +
594E SER 3.5 0.2 - - - -
595E ARG* 1.3 78.1 - - - +
597E VAL* 1.3 62.1 + - - +
598E GLU 3.3 0.3 + - - -
599E TRP* 3.4 2.8 + - - -
600E LYS* 3.2 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 597 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585E VAL* 3.7 22.7 - - + -
593E GLN 3.1 18.6 + - - +
594E SER* 4.3 7.6 - - - +
595E ARG 3.3 0.2 - - - -
596E ILE* 1.3 74.1 - - - +
598E GLU* 1.3 64.9 + - + +
600E LYS* 3.1 20.7 + - + +
601E GLU* 3.1 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 598 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594E SER* 3.1 18.0 + - - +
595E ARG* 3.1 34.6 - - - +
596E ILE 3.1 0.4 - - - -
597E VAL* 1.3 79.8 - - + +
599E TRP* 1.3 68.6 + - + +
601E GLU* 3.3 22.5 + - - +
602E ARG* 3.4 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 599 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369E LEU* 3.8 30.5 - - + +
372E MET* 3.6 46.9 - - + -
373E ASP* 3.2 33.5 + - - -
376E PHE* 3.9 20.4 - + + -
384E ILE* 5.0 4.5 - - + -
577E LEU* 4.9 0.2 - - + -
580E ILE* 4.1 20.9 - - + -
595E ARG* 3.6 20.6 - - + +
596E ILE 3.4 2.5 + - - +
598E GLU* 1.3 79.6 + - + +
600E LYS* 1.3 56.8 + - - +
601E GLU 2.9 6.1 - - - -
602E ARG* 3.6 29.6 - - + -
603E LEU* 2.9 61.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 600 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580E ILE* 2.7 36.1 + - + +
581E TRP 4.2 7.9 + - - -
582E TYR 4.6 1.2 + - - -
583E ARG 3.2 24.5 + - - -
584E PRO* 4.2 3.3 - - - +
585E VAL* 3.4 35.2 - - + +
596E ILE* 3.2 24.7 + - - +
597E VAL* 3.1 16.2 + - + +
599E TRP* 1.3 76.8 - - - +
601E GLU* 1.3 58.9 + - + +
603E LEU* 5.0 2.9 - - - -
604E ASP* 2.6 34.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 601 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597E VAL* 3.1 31.2 + - + +
598E GLU* 3.5 16.3 - - - +
599E TRP 2.9 0.4 - - - -
600E LYS* 1.3 81.3 - - + +
602E ARG* 1.3 59.6 + - - +
603E LEU 3.4 0.2 - - - -
604E ASP* 3.9 2.7 - - - +
605E LYS* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 602 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376E PHE* 3.5 31.1 + - - +
384E ILE* 4.6 17.0 - - + +
598E GLU 3.4 10.1 + - - +
599E TRP* 3.2 40.8 + - + +
601E GLU* 1.3 77.1 - - - +
603E LEU* 1.3 67.6 + - + +
605E LYS* 3.2 14.1 + - - +
606E GLU* 3.0 55.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 603 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384E ILE* 4.9 8.5 - - + -
388E MET* 3.7 16.4 - - + -
577E LEU* 3.6 34.5 - - + +
580E ILE* 5.0 7.4 - - + -
581E TRP* 3.6 37.6 - - + +
599E TRP* 2.9 57.7 + - + +
600E LYS* 5.0 2.5 - - - -
602E ARG* 1.3 80.9 - - + +
604E ASP* 1.3 57.8 + - - +
606E GLU* 3.4 3.8 + - - +
607E PHE* 2.8 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 604 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581E TRP* 5.1 9.7 - - - -
600E LYS* 2.6 29.7 + - - +
601E GLU* 3.7 4.2 + - - +
602E ARG 3.4 0.6 - - - -
603E LEU* 1.3 80.4 - - - +
605E LYS* 1.3 61.6 + - - +
607E PHE 3.3 18.3 - - - +
608E SER* 4.4 4.7 + - - -
609E LEU* 4.4 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 605 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601E GLU 3.0 20.0 + - - +
602E ARG* 3.3 15.7 - - - +
603E LEU 3.1 0.2 - - - -
604E ASP* 1.3 80.1 - - - +
606E GLU* 1.3 71.8 + - - +
607E PHE 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 606 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384E ILE* 4.6 13.5 - - + +
602E ARG* 3.0 48.1 + - + +
603E LEU* 4.1 2.5 - - - +
605E LYS* 1.3 91.4 - - + +
607E PHE* 1.3 84.3 + - + +
608E SER 4.4 0.3 + - - -
611E VAL* 5.5 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 607 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384E ILE* 4.1 13.7 - - + -
385E GLU* 3.4 52.3 - - + -
388E MET* 4.2 17.7 - - + -
581E TRP* 3.8 19.5 - - + -
603E LEU* 2.8 25.1 + - - +
604E ASP* 3.3 16.2 - - - +
605E LYS 5.2 0.2 - - - -
606E GLU* 1.3 99.5 - - + +
608E SER* 1.3 65.6 + - - +
611E VAL* 3.5 33.9 - - + -
612E TYR* 5.1 1.3 - - + +
615E MET* 4.2 21.3 - - + -
----------------------------------------------------------
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