Contacts of the helix formed by residues 989 - 1001 (chain A) in PDB entry 2OOQ
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 THR 989 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937A LYS* 3.8 42.4 - - + +
965A ILE* 5.6 6.7 - - + -
983A GLN* 4.0 6.0 + - - -
985A PRO* 3.7 6.2 - - - +
986A MET* 2.8 36.6 + - + +
988A GLU* 1.3 83.2 - - + +
990A VAL* 1.3 59.9 + - - +
991A LYS 3.2 2.9 - - - -
992A ASP* 3.0 19.9 + - - +
993A PHE* 2.8 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 990 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985A PRO* 4.0 7.6 - - + -
986A MET 3.1 15.5 + - - +
987A GLN 4.1 0.2 - - - +
988A GLU 3.6 1.4 - - - -
989A THR* 1.3 75.4 - - - +
991A LYS* 1.3 63.3 + - - +
993A PHE* 3.2 9.0 + - - +
994A TRP* 3.1 29.2 + - + -
1020A VAL* 3.4 24.7 - - + -
1021A ARG 4.6 1.6 - - - +
1022A TYR* 4.1 14.8 - - + -
1030A TYR* 3.5 32.8 - - + -
1059B HIS* 3.5 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 991 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987A GLN 4.8 2.4 + - - -
988A GLU* 4.0 19.8 + - - +
990A VAL* 1.3 80.8 - - - +
992A ASP* 1.3 66.4 + - - +
994A TRP* 3.3 3.3 + - - +
995A ARG* 2.9 30.4 + - - +
1030A TYR* 4.5 11.7 - - + +
1031A GLY* 3.9 21.7 - - - +
1054B GLN* 3.4 25.3 - - - +
1059B HIS* 4.2 22.4 + - + +
1061B ILE* 3.5 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 992 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937A LYS* 4.7 11.8 - - - +
953A LEU* 3.9 17.5 - - + +
964A TYR 4.5 10.2 - - - +
965A ILE* 3.8 13.1 - - + +
988A GLU 4.3 2.8 - - - +
989A THR* 3.0 28.7 + - - +
991A LYS* 1.3 84.3 - - - +
993A PHE* 1.3 58.7 + - - +
995A ARG* 3.3 20.9 + - - +
996A MET* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 993 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965A ILE* 3.8 13.6 - - + +
982A THR* 4.2 13.0 - - + -
983A GLN 5.0 1.3 - - - -
985A PRO* 3.6 32.1 - - + -
989A THR* 2.8 13.3 + - - +
990A VAL 3.4 8.1 - - - +
992A ASP* 1.3 76.9 - - - +
994A TRP* 1.3 66.7 + + - +
996A MET* 3.3 14.0 + - + +
997A ILE* 3.0 53.9 + - + +
1005A ILE* 4.1 9.6 - - + -
1022A TYR* 3.6 42.4 - + + -
1103A VAL* 4.0 24.5 - - + -
1105A HIS* 4.5 2.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 994 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
990A VAL* 3.1 26.8 + - + -
991A LYS 3.9 5.6 - - - +
993A PHE* 1.3 77.2 - + - +
995A ARG* 1.3 60.2 + - - +
997A ILE* 3.4 32.0 + - + +
998A TRP* 2.9 29.1 + - - +
1005A ILE* 4.3 12.3 - - + -
1022A TYR* 2.9 49.0 + + - +
1023A TRP* 4.7 4.3 - - + -
1030A TYR* 3.3 35.6 - + + +
1033A ILE* 3.9 22.3 - - + +
1035A VAL* 3.7 38.8 - - + -
1051A PHE* 5.3 3.4 - + - -
1053A VAL* 4.2 12.6 - - + -
1064A LEU* 4.4 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 995 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953A LEU* 3.5 25.5 - - + +
954A LEU* 2.7 33.1 + - - +
956A LEU* 3.5 41.5 - - - +
962A SER* 2.9 28.1 + - - -
991A LYS 2.9 16.9 + - - +
992A ASP* 3.6 18.4 + - - +
994A TRP* 1.3 76.1 - - - +
996A MET* 1.3 56.5 + - - +
998A TRP* 3.3 6.1 + - + +
999A GLN* 2.8 35.3 + - + +
1032A ASP* 5.9 2.0 - - - -
1033A ILE* 4.5 6.8 - - + +
1055A LYS* 5.7 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 996 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951A VAL* 3.7 32.8 - - + -
953A LEU* 3.7 16.5 - - + +
965A ILE* 4.0 19.3 - - + -
967A ALA* 3.8 18.6 - - - -
980A ILE* 4.0 20.9 - - + -
982A THR* 4.4 9.6 - - + -
992A ASP 2.9 14.3 + - - +
993A PHE* 3.5 16.4 - - + +
995A ARG* 1.3 72.7 - - - +
997A ILE* 1.3 58.7 + - + +
999A GLN* 3.6 2.9 - - - +
1000A GLU* 2.8 47.6 + - + +
1103A VAL* 4.2 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 997 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993A PHE* 3.0 48.9 + - + +
994A TRP* 3.5 28.7 - - + +
996A MET* 1.3 80.4 - - + +
998A TRP* 1.3 64.4 + - + +
1001A ASN* 3.2 18.0 + - - -
1002A SER* 3.3 22.8 + - - +
1005A ILE* 3.6 20.0 - - + -
1053A VAL* 5.2 6.1 - - + -
1062A ARG* 4.2 0.9 + - - -
1064A LEU* 3.6 24.2 - - + -
1103A VAL* 4.5 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 998 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994A TRP 2.9 17.4 + - - +
995A ARG* 3.7 4.9 - - + +
997A ILE* 1.3 75.5 - - - +
999A GLN* 1.3 68.6 + - - +
1000A GLU 3.2 0.5 + - - -
1001A ASN* 3.2 2.3 + - - +
1033A ILE* 3.8 17.3 - - + -
1053A VAL* 3.5 42.4 - - + -
1054A GLN* 3.8 2.0 - - - -
1055A LYS* 3.7 45.2 - - + +
1058A TYR* 5.7 4.3 - - + -
1060A GLU* 3.6 33.9 - - + -
1062A ARG* 2.9 71.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 999 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951A VAL* 4.7 0.8 - - - +
952A ARG 2.8 27.0 + - - -
953A LEU* 3.4 14.2 - - - +
954A LEU* 2.9 41.5 + - + +
995A ARG* 2.8 26.7 + - + +
996A MET 3.6 3.8 - - - +
998A TRP* 1.3 78.4 - - - +
1000A GLU* 1.3 82.3 + - - +
1001A ASN* 3.6 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1000 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951A VAL* 4.2 3.1 - - + -
969A TYR* 2.8 40.0 + - - -
980A ILE* 3.8 15.7 - - + +
996A MET* 2.8 32.3 + - + +
999A GLN* 1.3 103.1 + - + +
1001A ASN* 1.3 70.0 + - - +
1002A SER* 3.3 14.5 + - - +
1100A GLY* 3.3 14.9 - - - -
1101A PRO* 3.5 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1001 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997A ILE 3.2 3.8 + - - -
998A TRP 3.2 5.0 + - - +
999A GLN 3.3 1.5 - - - +
1000A GLU* 1.3 80.0 - - - +
1002A SER* 1.3 65.1 + - - +
1003A ALA* 3.6 1.2 + - - +
1060A GLU* 4.7 2.1 - - - +
1062A ARG* 3.3 44.1 + - - +
1098A GLU 4.5 4.4 + - - -
1099A ALA* 3.6 20.5 - - - +
1100A GLY* 2.8 18.6 + - - +
----------------------------------------------------------
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