Contacts of the helix formed by residues 672 - 683 (chain A) in PDB entry 3RC3
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 ASN 672 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A ASP* 3.0 17.9 + - - +
669A GLY* 2.9 13.4 + - - +
671A HIS* 1.3 95.4 + - - +
673A ILE* 1.4 62.4 + - - +
674A THR* 3.2 4.7 - - - -
675A LYS* 2.9 50.7 + - + +
676A LEU* 3.3 13.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 673 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ILE* 5.4 0.2 - - + -
379A TYR* 4.2 23.8 - - + -
382A SER* 4.7 0.2 - - - +
394A VAL* 3.9 33.0 - - + -
396A TYR* 4.2 15.3 - - + -
407A GLN* 6.0 0.2 - - - +
622A ILE* 5.6 1.6 - - + -
625A LEU* 4.1 27.8 - - + -
669A GLY 3.0 4.4 + - - -
670A VAL* 2.9 26.6 + - + +
671A HIS 3.3 1.4 + - - -
672A ASN* 1.4 77.0 - - - +
674A THR* 1.3 62.7 + - + +
676A LEU* 3.0 9.3 + - + +
677A ILE* 2.9 42.2 + - + +
901A NA 4.0 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 674 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A SER* 3.8 35.2 - - - +
383A ARG* 4.0 6.9 - - - +
386A GLU* 2.6 40.8 + - + +
392A SER* 5.5 2.2 - - - +
671A HIS 5.1 2.2 + - - -
672A ASN* 4.6 2.4 + - - -
673A ILE* 1.3 79.1 - - + +
675A LYS* 1.3 62.6 + - - +
677A ILE* 3.7 7.6 - - - +
678A LYS* 2.9 28.9 + - - +
901A NA 4.2 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 675 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A GLU* 5.4 2.7 - - - +
672A ASN* 2.9 41.6 + - + +
674A THR* 1.3 80.7 + - - +
676A LEU* 1.3 67.4 + - + +
678A LYS* 3.8 9.9 - - + +
679A MSE 3.0 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 676 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A PRO* 3.3 43.5 - - + +
620A LYS* 3.5 19.7 - - - +
621A ASN* 3.6 18.3 - - - +
622A ILE* 3.9 7.0 - - + +
625A LEU* 4.0 26.2 - - + -
669A GLY* 3.5 19.5 - - - +
672A ASN* 3.7 15.3 - - + +
673A ILE* 3.0 10.2 + - + +
675A LYS* 1.3 78.5 - - + +
677A ILE* 1.3 58.2 + - - +
679A MSE 3.1 4.0 + - - +
680A SER* 2.8 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 677 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A TYR* 3.5 32.5 - - + +
382A SER* 3.1 28.5 - - - +
383A ARG* 4.0 8.1 - - + +
622A ILE* 3.9 23.8 - - + -
673A ILE* 2.9 33.5 + - + +
674A THR* 3.7 8.1 - - - +
676A LEU* 1.3 77.1 - - - +
678A LYS* 1.3 58.6 + - - +
680A SER* 3.0 3.5 + - - -
681A GLU* 2.9 34.1 + - - +
688A LEU* 3.7 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 678 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ARG* 3.8 40.1 - - - +
386A GLU* 5.2 4.0 - - - +
674A THR 2.9 18.0 + - - +
675A LYS* 3.9 9.6 - - + +
677A ILE* 1.3 76.4 - - - +
679A MSE 1.3 56.0 + - - +
681A GLU 4.5 0.2 - - - +
682A THR* 2.6 55.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 679 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A LYS* 3.1 37.2 - - + +
621A ASN* 4.2 9.0 - - + +
675A LYS* 3.0 19.3 + - + +
676A LEU 3.5 2.2 - - - +
678A LYS* 1.3 74.7 - - + +
680A SER* 1.3 67.8 + - - +
682A THR* 4.1 2.2 - - - -
683A HIS* 2.8 73.2 + - + +
684A LYS* 3.1 6.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 680 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A ASN* 3.4 6.3 - - - +
622A ILE* 3.0 49.0 + - - +
623A LYS* 4.4 1.2 + - - +
676A LEU 2.8 9.0 + - - -
677A ILE 3.0 7.1 + - - -
679A MSE 1.3 77.0 - - - +
681A GLU* 1.3 57.2 + - - +
684A LYS* 3.2 16.2 - - - +
685A LEU 3.0 22.2 + - - -
686A LEU* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 681 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ARG* 2.9 37.0 + - - +
677A ILE* 2.9 15.5 + - - +
678A LYS 3.9 2.7 - - - +
680A SER* 1.3 77.9 - - - +
682A THR* 1.3 67.5 + - + +
685A LEU* 3.1 25.3 - - - +
686A LEU 3.7 19.9 - - - +
688A LEU* 3.2 39.9 + - + +
689A GLU* 4.9 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 682 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ARG* 4.5 7.9 - - - +
678A LYS* 2.6 53.7 + - + +
679A MSE 4.1 0.9 - - - -
681A GLU* 1.3 81.9 - - + +
683A HIS* 1.3 76.2 + - - +
685A LEU* 3.9 13.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 683 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A MSE 2.8 50.9 + - + +
682A THR* 1.3 95.3 + - - +
684A LYS* 1.3 72.8 + - + +
685A LEU* 3.3 8.1 + - - +
----------------------------------------------------------
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