Contacts of the helix formed by residues 960 - 971 (chain A) in PDB entry 2EYQ
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 GLY 960 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956A GLY 2.8 19.0 + - - -
957A GLU* 4.1 3.6 + - - -
958A LEU 3.8 0.6 - - - -
959A LEU* 1.3 77.3 - - - +
961A GLU* 1.3 56.5 + - - -
962A GLU* 2.8 9.2 - - - -
963A GLN* 2.7 25.0 + - - -
964A SER* 2.8 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 961 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
960A GLY* 1.3 71.2 - - - -
962A GLU* 1.3 60.1 + - - +
964A SER* 3.7 11.0 + - - -
965A GLY* 3.5 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 962 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A LYS* 4.6 14.1 - - + +
563A ASP* 5.7 3.2 - - - +
564A VAL* 5.2 2.1 - - - +
960A GLY* 2.8 2.2 - - - -
961A GLU* 1.3 81.9 - - - +
963A GLN* 1.3 80.7 + - + +
965A GLY* 3.5 8.5 + - - -
966A SER* 3.9 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 963 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A LYS* 3.8 14.1 - - - +
561A VAL* 4.2 9.2 + - - -
564A VAL* 3.1 35.1 - - + +
959A LEU* 3.7 31.4 - - + +
960A GLY* 2.7 14.7 + - - +
962A GLU* 1.3 101.9 + - + +
964A SER* 1.3 62.5 + - - +
965A GLY 2.8 6.4 + - - -
966A SER* 3.3 7.9 + - - -
967A MET* 3.0 27.9 + - + +
975A TYR* 2.5 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 964 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956A GLY* 3.0 29.3 + - - -
960A GLY 2.8 14.5 + - - -
961A GLU* 3.9 10.2 - - - -
962A GLU 3.5 0.2 - - - -
963A GLN* 1.3 77.7 - - - +
965A GLY* 1.3 55.6 + - - +
967A MET* 3.3 15.4 - - - +
968A GLU* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 965 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961A GLU 3.5 7.1 + - - -
962A GLU 3.5 8.6 + - - -
963A GLN 2.8 2.8 - - - -
964A SER* 1.3 75.7 - - - +
966A SER* 1.3 55.5 + - - -
967A MET 3.0 1.3 - - - -
968A GLU* 2.9 12.0 + - - +
969A THR* 2.7 38.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 966 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A ALA 5.7 0.4 - - - -
556A LYS* 6.2 3.1 - - - -
557A ALA* 3.9 32.5 + - - +
560A LYS* 5.2 6.0 - - - +
962A GLU 3.9 6.4 + - - -
963A GLN* 3.3 9.4 + - - -
965A GLY* 1.3 73.5 - - - +
967A MET* 1.3 63.7 + - - +
969A THR* 3.9 8.0 - - - -
970A ILE* 3.0 32.9 + - - +
975A TYR* 3.2 23.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 967 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A TYR* 4.7 0.2 + - - -
534A GLY* 4.6 5.4 - - - -
952A ILE* 4.2 13.5 - - + -
955A ALA* 4.0 6.5 - - + -
956A GLY* 3.9 29.2 - - - +
959A LEU* 3.6 30.7 - - + -
963A GLN* 3.0 18.8 + - + +
964A SER* 3.3 11.0 - - - +
966A SER* 1.3 79.4 + - - +
968A GLU* 1.3 58.4 + - - +
970A ILE* 4.8 0.2 - - - -
971A GLY* 3.1 27.9 + - - -
972A PHE* 3.6 31.0 + - + -
975A TYR* 3.7 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 968 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A TYR* 2.4 32.6 + - - +
534A GLY* 4.8 9.2 - - - -
536A ALA* 4.0 21.3 - - + +
539A ASN* 4.3 14.0 + - - +
541A PRO* 3.8 8.0 - - + +
964A SER 2.9 16.4 + - - +
965A GLY* 2.9 9.7 + - - +
967A MET* 1.3 76.7 - - - +
969A THR* 1.3 59.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 969 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A VAL* 4.3 1.6 - - - +
532A TYR* 5.1 1.1 - - - -
541A PRO* 4.0 14.6 - - + +
543A HIS* 3.8 23.8 + - + -
550A TRP* 3.9 2.3 - - - -
553A ALA* 4.1 22.4 - - + -
965A GLY 2.7 22.9 + - - -
966A SER* 3.2 8.5 + - - -
968A GLU* 1.3 82.3 - - - +
970A ILE* 1.3 61.9 + - - +
971A GLY 3.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 970 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A VAL* 4.1 15.9 - - - +
490A VAL* 5.1 0.7 - - - -
532A TYR* 4.6 4.9 - - - -
550A TRP* 3.9 31.7 - - + -
553A ALA* 4.0 25.1 - - + +
554A ARG* 4.6 3.6 - - - -
557A ALA* 3.9 20.6 - - + -
966A SER* 3.0 17.0 + - - +
969A THR* 1.3 85.8 - - - +
971A GLY* 1.3 68.1 + - - +
974A LEU* 4.1 20.4 - - + +
975A TYR* 3.9 31.0 - - + +
978A LEU* 4.5 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 971 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A VAL* 5.2 2.0 - - - -
531A ARG 5.8 0.2 - - - -
532A TYR* 4.0 23.2 - - - -
533A ALA 4.4 4.7 - - - -
534A GLY 4.8 0.2 - - - -
967A MET 3.1 12.5 + - - -
969A THR 3.8 0.6 - - - -
970A ILE* 1.3 80.4 - - - +
972A PHE* 1.3 68.5 + - - -
973A SER* 2.7 7.4 + - - -
974A LEU 2.9 14.5 + - - -
975A TYR* 3.1 8.4 + - - +
----------------------------------------------------------
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