Contacts of the helix formed by residues 660 - 673 (chain A) in PDB entry 2RD0
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 660 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A MET 5.5 0.2 - - - -
165A TYR* 4.0 3.6 - - - -
168A PRO* 3.0 29.7 - - - +
625A ASP* 2.9 42.0 + - - +
656A LYS* 2.9 6.2 + - + +
657A ALA 3.8 2.7 - - - +
659A THR* 1.3 79.9 - - + +
661A GLN* 1.3 57.5 + - - +
662A ARG* 3.0 21.9 + - - +
663A ILE* 2.9 41.4 + - + +
664A GLY 3.0 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 661 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 3.0 59.6 + - + +
166A VAL* 3.8 31.4 - - - +
167A TYR 5.0 0.2 - - - +
168A PRO* 4.9 0.9 - - + -
299A MET* 4.8 2.3 - - - +
660A ASN* 1.3 73.5 + - - +
662A ARG* 1.3 61.8 + - - +
664A GLY* 3.7 3.6 - - - +
665A HIS* 3.2 20.4 + - - +
691A TYR* 5.1 2.2 - - - +
695A CYS 4.1 0.3 - - - +
698A TYR* 3.2 57.0 + - + +
701A HIS* 5.5 1.0 + - - -
757A PRO* 5.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 662 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PRO* 3.7 30.1 + - + +
169A PRO 2.9 30.5 + - - -
170A ASN* 3.4 36.1 + - - +
171A VAL 4.8 0.6 - - - +
259A GLU* 5.9 1.8 - - - +
625A ASP* 5.8 0.8 + - - +
629A SER* 4.8 19.2 + - - -
660A ASN* 3.0 15.9 + - - +
661A GLN* 1.3 79.8 - - - +
663A ILE* 1.3 61.5 + - - +
665A HIS* 3.6 7.0 + - - +
666A PHE* 3.6 32.2 - - + -
757A PRO* 5.8 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 663 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A ASP* 4.2 15.3 - - + +
628A LEU* 3.6 31.2 - - + -
629A SER* 3.9 19.5 - - - +
632A LEU* 4.2 27.7 - - + +
653A LEU* 5.5 1.1 - - + +
656A LYS* 4.4 6.7 - - + -
657A ALA* 3.9 20.9 - - + +
660A ASN* 2.9 38.6 + - + +
662A ARG* 1.3 75.6 - - + +
664A GLY* 1.3 67.7 + - - +
665A HIS 3.0 2.1 + - - -
666A PHE* 3.2 2.5 + - - +
667A PHE* 2.9 24.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 664 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A ALA* 3.3 25.6 + - - -
660A ASN 3.0 10.3 + - - -
661A GLN* 3.5 4.9 + - - -
663A ILE* 1.3 75.7 - - - +
665A HIS* 1.3 56.3 + - - +
667A PHE* 3.6 1.0 - - - +
668A PHE* 2.8 32.4 + - - +
691A TYR* 3.3 24.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 665 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A GLN 3.2 11.9 + - - +
662A ARG 3.7 10.1 - - - +
663A ILE 3.0 0.8 + - - -
664A GLY* 1.3 76.5 - - - +
666A PHE* 1.3 87.1 + + - +
668A PHE* 3.2 5.7 + - - +
669A TRP* 2.9 40.4 + + - -
691A TYR* 4.2 0.4 + - - -
698A TYR* 2.7 34.5 + - + +
702A LEU* 4.3 0.6 - - - +
705A GLN* 2.8 26.3 + - - -
753A SER 4.2 0.7 - - - -
754A PRO* 2.9 34.9 + - + +
757A PRO* 3.9 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 666 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A SER* 6.1 5.6 - - - -
632A LEU* 3.7 19.1 - - + -
662A ARG* 3.6 25.1 + - + -
663A ILE* 3.2 4.3 + - - +
665A HIS* 1.3 92.4 - + - +
667A PHE* 1.3 57.3 + - - +
669A TRP* 4.2 2.2 - - + +
670A HIS* 2.7 51.4 + + - +
754A PRO 3.6 16.6 - - - -
755A LEU* 3.6 23.6 - - - -
756A ASN* 4.8 0.4 - - - -
757A PRO* 4.5 8.1 - - + -
839A LEU* 4.0 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 667 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A LEU* 3.5 18.4 - - + +
636A VAL* 4.2 20.0 - - + -
639A LEU* 5.1 0.2 - - + -
653A LEU* 4.1 22.4 - - + -
654A LEU* 4.3 13.9 - - + -
657A ALA* 3.3 26.7 - - + -
663A ILE* 2.9 20.1 + - + +
664A GLY 3.6 1.6 - - - +
666A PHE* 1.3 73.5 - - - +
668A PHE* 1.3 68.4 + - - +
670A HIS* 4.1 2.4 - - - +
671A LEU* 3.2 50.9 + - + +
687A LEU* 3.7 28.7 - - + -
691A TYR* 4.0 28.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 668 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ALA* 3.4 41.5 - - + -
121A ILE 4.9 0.2 - - - -
664A GLY 2.8 18.5 + - - +
665A HIS 3.4 7.2 - - - +
667A PHE* 1.3 76.7 - - - +
669A TRP* 1.3 97.9 + + - +
671A LEU* 3.2 1.9 + - - +
672A LYS* 2.8 39.7 + - + +
688A LEU* 3.5 30.7 - - + +
691A TYR* 4.2 7.0 - + + -
692A CYS* 4.3 11.0 - - - -
702A LEU* 3.7 37.9 - - + -
706A VAL* 3.9 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 669 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A HIS* 2.9 46.0 + + - +
666A PHE* 4.1 4.0 - - - +
668A PHE* 1.3 94.9 - + - +
670A HIS* 1.3 56.8 + - - +
672A LYS* 3.8 11.0 - - + +
673A SER* 2.9 32.3 + - - -
702A LEU* 3.7 6.1 - - - +
705A GLN* 3.2 37.1 + - + -
706A VAL* 3.6 31.0 - - + -
709A MET* 4.1 18.6 - - + -
754A PRO* 4.1 12.0 - - + +
839A LEU* 4.2 24.7 - - + -
840A SER 4.3 1.2 - - - +
841A ILE* 3.7 41.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 670 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A LEU* 3.8 25.8 - - + +
633A ILE* 4.3 26.9 + - + +
636A VAL* 4.5 24.2 - - + +
637A GLN* 5.2 2.0 + - - +
666A PHE* 2.7 41.5 + + - +
667A PHE 4.2 2.2 - - - +
669A TRP* 1.3 72.7 - - - +
671A LEU* 1.3 61.4 + - - +
673A SER* 3.7 13.2 - - - -
674A GLU* 4.2 11.3 + - - +
684A PHE* 5.0 0.3 - - - -
811A MET* 3.4 34.2 - - + +
839A LEU* 3.9 20.6 - - + +
840A SER 5.3 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 671 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A VAL* 4.2 15.0 - - + -
639A LEU* 4.8 1.1 - - + -
667A PHE* 3.2 54.3 + - + +
668A PHE 3.6 0.4 - - - +
670A HIS* 1.3 75.0 - - - +
672A LYS* 1.3 66.8 + - - +
673A SER 3.1 1.6 - - - -
674A GLU* 3.0 14.7 + - - -
675A MET* 3.6 8.5 + - - +
684A PHE* 3.5 50.3 - - + -
687A LEU* 4.0 18.4 - - + -
688A LEU* 3.6 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 672 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE 3.8 8.5 + - - -
120A ALA 2.7 32.4 + - - +
121A ILE 3.2 24.2 - - - +
122A GLY* 4.1 6.7 - - - +
668A PHE* 2.8 40.7 + - + +
669A TRP* 3.9 11.9 - - + +
671A LEU* 1.3 73.0 - - - +
673A SER* 1.3 64.0 + - - +
674A GLU 2.9 1.6 + - - -
675A MET* 3.0 18.5 + - + +
688A LEU* 3.6 11.7 - - + +
706A VAL* 4.1 18.6 - - - +
710A GLU* 5.3 4.2 + - - -
841A ILE 4.6 9.2 - - - +
842A GLY* 4.9 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 673 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A TRP 2.9 19.1 + - - -
670A HIS* 3.7 12.3 - - - -
671A LEU 3.1 0.2 - - - -
672A LYS* 1.3 75.6 - - - +
674A GLU* 1.3 64.2 + - - +
676A HIS* 3.3 14.4 + - - -
808A ARG* 5.4 3.1 - - - +
811A MET* 6.3 0.7 - - - -
840A SER* 3.2 37.9 + - - -
841A ILE 3.8 2.9 + - - -
842A GLY* 3.2 29.6 + - - +
----------------------------------------------------------
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