Contacts of the helix formed by residues 613 - 627 (chain C) in PDB entry 1DE4
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 613 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500C PRO* 3.2 35.0 - - + +
503C TYR* 3.5 28.7 - - + +
504C THR* 2.9 37.4 + - - +
507C GLU* 3.4 24.7 + - - -
528C TRP* 4.9 1.2 - - - -
529C ALA* 4.0 20.4 - - - +
610C ASP* 3.4 22.6 + - + +
611C TYR 3.1 0.4 - - - -
612C GLU* 1.3 82.3 - - - +
614C TYR* 1.3 59.9 + - - +
615C ASN 3.2 1.0 + - - -
616C SER* 3.5 18.7 + - - +
617C GLN* 3.7 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 614 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500C PRO* 3.6 25.1 - - + +
501C LEU* 3.8 32.8 - - + -
611C TYR 3.3 4.1 + - - +
612C GLU 2.9 2.0 + - - -
613C ARG* 1.3 76.9 - - - +
615C ASN* 1.3 60.3 + - - +
616C SER 3.2 0.2 - - - -
617C GLN* 3.3 10.4 + - + +
618C LEU* 3.0 31.4 + - - +
649C PHE* 3.6 23.6 - - + -
681C VAL* 4.5 6.1 - - + -
682C GLU* 2.6 29.8 + - - -
685C PHE* 3.3 33.2 - + + -
699C HIS* 3.4 2.6 + - - -
701C PHE* 3.8 31.6 - + - -
702C TRP* 3.2 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 615 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A HIS* 3.7 7.2 - - + -
611C TYR 4.7 0.2 + - - -
612C GLU* 2.9 41.5 + - - +
614C TYR* 1.3 79.7 - - - +
616C SER* 1.3 58.0 + - - +
618C LEU* 3.5 6.1 + - - +
619C LEU* 3.0 29.3 + - - +
646C ARG* 4.4 3.3 + - - +
649C PHE* 3.7 8.7 - - - -
650C PHE* 3.1 55.4 + - + +
653C THR* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 616 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.7 14.1 - - - +
74A HIS* 4.0 16.3 + - - -
612C GLU* 4.7 6.8 + - - -
613C ARG* 3.5 14.1 + - - -
614C TYR 3.2 0.6 - - - -
615C ASN* 1.3 78.1 - - - +
617C GLN* 1.3 59.7 + - - +
619C LEU* 4.4 1.8 - - - -
620C SER* 3.0 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 617 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500C PRO* 3.5 31.6 - - + +
503C TYR* 4.0 17.8 + - - -
529C ALA 5.9 0.2 + - - -
613C ARG 3.9 9.4 - - - +
614C TYR* 3.3 12.9 + - + +
615C ASN 3.3 0.4 - - - -
616C SER* 1.3 76.0 - - - +
618C LEU* 1.3 65.5 + - - +
620C SER* 3.3 9.7 + - - -
621C PHE* 3.1 21.3 + - - +
701C PHE* 3.7 23.5 - - + -
702C TRP* 3.6 27.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 618 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614C TYR 3.0 14.8 + - - +
615C ASN* 3.7 6.1 - - - +
617C GLN* 1.3 74.2 - - - +
619C LEU* 1.3 65.4 + - - +
621C PHE* 2.9 18.1 + - + +
622C VAL* 3.0 16.7 + - - +
646C ARG* 3.8 26.2 - - + +
649C PHE* 3.7 44.2 - - + -
685C PHE* 5.1 4.7 - - + -
701C PHE* 3.1 32.8 - - + -
709C LEU* 5.2 1.8 - - + -
742C ILE* 4.0 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 619 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.4 24.7 - - + -
23A SER* 3.9 19.1 - - - +
74A HIS* 3.7 48.2 - - + +
77A THR* 4.4 2.7 - - + -
78A VAL* 3.6 31.2 - - + -
81A TRP* 3.6 20.0 - - + -
615C ASN 3.0 18.7 + - - +
616C SER 3.9 0.2 - - - +
618C LEU* 1.3 74.1 - - - +
620C SER* 1.3 58.6 + - - +
622C VAL* 3.0 10.2 + - - +
623C ARG 2.9 23.6 + - - -
646C ARG* 4.7 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 620 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.7 15.7 - - - +
616C SER 3.0 19.9 + - - -
617C GLN* 3.5 10.8 - - - -
619C LEU* 1.3 74.3 - - - +
621C PHE* 1.3 59.1 + - - +
623C ARG* 3.2 17.0 + - - +
624C ASP* 2.9 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 621 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617C GLN 3.1 11.5 + - - +
618C LEU* 2.9 14.8 + - + +
620C SER* 1.3 76.5 - - - +
622C VAL* 1.3 63.8 + - + +
624C ASP* 3.2 9.4 + - - +
625C LEU* 3.1 32.4 + - + +
642C LEU* 3.6 39.5 - - + -
701C PHE* 5.3 1.3 - - + -
709C LEU* 3.5 62.8 - - + -
712C LEU* 4.2 17.9 - - + -
713C LEU* 4.2 23.1 - - + -
735C LEU* 6.3 0.4 - - + -
738C ALA* 5.2 2.2 - - + -
742C ILE* 4.9 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 622 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A VAL* 3.9 18.6 - - + -
81A TRP* 4.0 10.3 - - + -
618C LEU 3.0 12.4 + - - +
619C LEU* 3.0 10.4 + - - +
621C PHE* 1.3 79.9 - - + +
623C ARG* 1.3 62.2 + - - +
625C LEU* 3.2 15.9 + - - +
626C ASN* 3.3 13.7 + - - +
642C LEU* 4.7 13.2 - - + -
643C TYR* 3.3 39.2 + - + +
646C ARG* 4.1 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 623 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU 5.5 1.2 + - - -
21A GLY* 4.4 3.0 - - - -
22A LEU* 3.5 40.6 - - - +
81A TRP* 3.4 40.8 - - + +
619C LEU 2.9 7.5 + - - +
620C SER* 3.5 20.0 + - - +
621C PHE 3.2 0.2 - - - -
622C VAL* 1.3 72.9 - - - +
624C ASP* 1.3 67.4 + - - +
625C LEU 2.9 8.3 + - - -
626C ASN* 2.6 35.9 - - - +
627C GLN* 4.5 0.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 624 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620C SER* 2.9 33.0 + - - +
621C PHE* 3.2 10.0 + - - +
623C ARG* 1.3 86.4 + - - +
625C LEU* 1.3 57.8 + - - +
626C ASN 3.7 0.2 - - - -
627C GLN* 3.8 11.8 - - - +
628C TYR* 3.8 20.3 - - - -
713C LEU* 3.5 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 625 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621C PHE* 3.1 25.4 + - + +
622C VAL* 3.4 8.3 - - + +
623C ARG 2.9 2.4 - - - -
624C ASP* 1.3 77.9 - - - +
626C ASN* 1.3 61.7 + - - +
627C GLN 3.2 2.7 - - - -
628C TYR* 3.2 16.9 + - + -
629C ARG* 3.6 9.6 + - - +
632C ILE* 5.6 1.6 - - + -
639C LEU* 3.9 25.6 - - + +
642C LEU* 3.3 33.9 - - + -
643C TYR* 5.5 0.7 - - + -
712C LEU* 4.0 6.7 - - + -
713C LEU* 3.2 27.8 - - + -
716C LEU* 3.9 22.7 - - + -
735C LEU* 5.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 626 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A TRP* 3.4 48.1 - - + +
85A GLU* 4.0 11.0 - - + +
622C VAL* 3.3 6.2 + - - +
623C ARG* 2.6 32.4 + - - +
625C LEU* 1.3 72.6 - - - +
627C GLN* 1.3 69.4 + - - +
628C TYR 3.0 6.0 + - - -
629C ARG* 3.1 40.7 + - - +
630C ALA 4.9 0.2 + - - -
643C TYR* 4.8 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 627 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623C ARG 4.5 0.6 + - - +
624C ASP* 3.8 10.7 - - - +
625C LEU 3.2 1.0 - - - -
626C ASN* 1.3 84.1 + - - +
628C TYR* 1.3 101.0 + - + +
629C ARG 3.5 0.8 + - - -
630C ALA* 4.9 4.9 + - - +
631C ASP* 4.3 0.3 - - - +
717C LYS* 5.8 2.8 - - - +
720C LYS* 3.5 23.8 + - - +
----------------------------------------------------------
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