Contacts of the helix formed by residues 949 - 967 (chain A) in PDB entry 2QEP
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 ALA 949 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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779A VAL* 3.8 21.5 - - + -
945A CYS* 3.8 0.8 - - - -
947A ASP* 2.7 23.8 + - - +
948A GLY* 1.3 74.8 - - - +
950A GLY* 1.3 60.2 + - - +
951A ARG 3.7 0.4 - - - -
952A SER 4.2 0.2 - - - -
953A GLY* 2.8 24.7 + - - -
986A PRO 3.8 3.1 - - - +
987A GLY* 3.6 24.0 - - - +
988A MET* 3.5 5.9 - - - -
989A VAL 3.1 14.3 + - - -
990A GLN* 5.8 0.7 - - + -
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Residues in contact with GLY 950 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947A ASP* 3.0 10.1 + - - -
949A ALA* 1.3 83.1 - - - +
951A ARG* 1.3 60.5 + - - +
954A THR* 2.9 24.4 + - - -
989A VAL* 3.7 2.6 - - - -
990A GLN* 3.8 27.6 - - - -
994A GLN* 3.5 14.4 - - - +
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Residues in contact with ARG 951 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A LEU* 3.3 22.1 + - + +
846A THR* 3.1 33.4 + - - +
847A PRO* 4.1 0.2 - - - +
850A GLU* 3.3 4.2 + - - -
855A GLN* 3.5 10.9 + - - -
911A TRP* 2.6 79.5 + - + +
912A TYR 3.9 4.5 - - - +
913A ASP* 3.2 28.4 + - - +
914A ARG 4.6 2.2 - - - +
945A CYS* 4.1 12.6 - - + +
946A SER* 3.3 31.3 - - - +
950A GLY* 1.3 72.7 - - - +
952A SER* 1.3 66.0 + - - +
953A GLY 3.1 0.2 - - - -
954A THR 3.0 2.4 + - - -
955A TYR 2.9 19.6 + - - -
994A GLN* 3.9 10.5 - - - +
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Residues in contact with SER 952 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A ALA* 4.9 4.0 - - - -
845A LEU* 3.6 10.0 - - - +
943A VAL* 3.6 13.6 - - - +
944A HIS* 3.2 12.6 - - - -
945A CYS* 3.0 39.8 + - - +
948A GLY* 3.6 20.1 - - - -
951A ARG* 1.3 78.8 - - - +
953A GLY* 1.3 55.4 + - - +
955A TYR* 3.5 2.6 + - - +
956A VAL* 2.9 34.0 + - - +
988A MET* 4.8 0.7 - - - -
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Residues in contact with GLY 953 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949A ALA 2.8 21.6 + - - -
952A SER* 1.3 76.0 - - - +
954A THR* 1.3 59.3 + - - +
955A TYR 3.2 0.2 - - - -
956A VAL* 3.7 1.0 - - - +
957A LEU* 2.8 32.6 + - - +
981A LEU* 4.1 2.6 - - - +
988A MET* 3.7 24.0 - - - +
989A VAL* 3.8 12.1 - - - +
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Residues in contact with THR 954 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911A TRP* 3.6 11.4 - - + -
950A GLY 2.9 15.9 + - - -
951A ARG 3.0 7.7 + - - -
953A GLY* 1.3 73.8 - - - +
955A TYR* 1.3 61.2 + - - +
957A LEU* 3.9 2.1 - - - +
958A ILE* 2.9 53.9 + - + +
989A VAL* 3.8 13.1 - - + +
994A GLN* 3.5 39.3 - - - +
997A PHE* 3.8 12.6 - - + -
998A ALA* 3.6 6.7 - - + -
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Residues in contact with TYR 955 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816A TYR* 5.0 3.6 - + - -
843A VAL* 4.3 13.7 - - + -
845A LEU* 3.5 30.3 - - + -
911A TRP* 3.9 5.3 - + + -
923A LEU* 4.1 20.4 - - + -
926A PHE* 3.9 24.5 - + - -
927A ARG* 3.6 28.5 - - + +
930A VAL* 3.5 31.1 - - + +
931A ASN* 4.9 1.4 + - - -
941A ILE* 5.6 2.0 - - + -
943A VAL* 4.2 22.2 - - + -
951A ARG 2.9 5.3 + - - -
952A SER 3.6 4.5 - - - +
954A THR* 1.3 76.7 - - - +
956A VAL* 1.3 55.2 + - - +
958A ILE* 3.1 10.4 + - + +
959A ASP* 2.7 54.0 + - + +
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Residues in contact with VAL 956 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806A ILE* 4.4 4.3 - - + -
816A TYR* 3.8 44.4 + - + -
818A ALA* 5.5 3.8 - - + -
943A VAL* 4.5 14.6 - - + -
952A SER* 2.9 24.8 + - - +
953A GLY* 3.8 7.2 - - - +
954A THR 3.4 0.2 - - - -
955A TYR* 1.3 75.9 - - - +
957A LEU* 1.3 53.8 + - - +
959A ASP* 3.1 6.0 + - - +
960A MET* 2.7 38.0 + - - +
981A LEU* 3.7 25.4 - - + -
988A MET* 4.5 9.0 - - + -
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Residues in contact with LEU 957 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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953A GLY 2.8 21.7 + - - +
954A THR 3.9 2.7 - - - +
956A VAL* 1.3 74.5 - - - +
958A ILE* 1.3 62.5 + - - +
960A MET* 3.4 2.7 + - - +
961A VAL* 3.1 36.2 + - + +
974A ILE* 4.0 20.0 - - + +
977A THR* 3.7 25.6 - - + -
978A LEU* 4.0 22.0 - - + +
981A LEU* 3.9 11.4 - - + +
989A VAL* 4.0 8.1 - - + -
995A PHE* 3.8 33.7 - - + -
998A ALA* 4.0 14.4 - - + -
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Residues in contact with ILE 958 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923A LEU* 4.6 10.1 - - + -
924A LEU* 4.4 14.1 - - + -
927A ARG* 4.6 6.5 - - - -
954A THR* 2.9 45.5 + - + +
955A TYR* 3.5 9.2 - - + +
957A LEU* 1.3 73.0 - - - +
959A ASP* 1.3 64.9 + - - +
961A VAL 3.6 0.2 + - - -
962A LEU* 3.4 40.2 + - + +
997A PHE* 3.7 18.6 - - + -
998A ALA* 3.4 31.9 - - - +
1001A ALA* 4.0 6.5 - - + -
1002A VAL* 4.1 13.8 - - + +
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Residues in contact with ASP 959 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816A TYR* 2.5 31.7 + - - +
927A ARG* 2.7 38.2 + - - +
931A ASN* 3.4 21.0 + - - +
941A ILE* 5.3 1.7 - - - +
955A TYR* 2.7 37.1 + - + +
956A VAL* 3.7 2.5 - - - +
958A ILE* 1.3 75.4 - - - +
960A MET* 1.3 63.8 + - - +
962A LEU 3.7 0.2 + - - -
963A ASN* 3.1 31.8 + - - +
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Residues in contact with MET 960 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806A ILE* 5.0 0.9 - - - -
807A MET 4.0 7.0 - - - +
808A ASP* 3.0 54.2 - - + +
816A TYR* 3.7 21.3 - - + +
956A VAL* 2.7 23.7 + - - +
957A LEU 3.9 2.9 - - - +
959A ASP* 1.3 73.4 - - - +
961A VAL* 1.3 62.7 + - - +
963A ASN* 3.6 7.5 + - - +
964A LYS* 3.4 19.2 + - - +
977A THR* 4.6 19.3 - - + -
980A HIS* 4.3 14.1 - - + -
981A LEU* 4.0 28.9 - - - -
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Residues in contact with VAL 961 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731A ILE* 4.9 12.4 - - + +
957A LEU* 3.1 36.1 + - + +
959A ASP 3.3 0.4 - - - -
960A MET* 1.3 75.2 - - - +
962A LEU* 1.3 65.9 + - - +
964A LYS* 3.3 16.8 + - + +
965A MET* 3.3 9.7 + - - +
972A ILE* 5.7 6.5 - - + -
974A ILE* 4.2 28.5 - - + -
977A THR* 4.2 13.5 - - + +
1002A VAL* 4.1 30.3 - - + -
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Residues in contact with LEU 962 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731A ILE* 5.7 0.4 - - + -
924A LEU* 4.0 17.7 - - + -
927A ARG* 3.3 39.4 + - - +
958A ILE* 3.4 21.7 + - + +
961A VAL* 1.3 75.1 - - - +
963A ASN* 1.3 57.1 + - - +
965A MET* 3.0 13.7 + - + +
966A ALA* 2.8 26.9 + - - +
1002A VAL* 4.1 18.4 - - + +
1005A GLU* 3.8 30.3 - - + -
1006A VAL* 3.9 24.7 - - + -
1009A ILE* 5.5 1.1 - - + -
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Residues in contact with ASN 963 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808A ASP* 5.1 9.1 + - - +
816A TYR* 4.0 6.7 + - - -
927A ARG* 3.4 16.3 + - - -
931A ASN* 4.8 4.7 + - - +
959A ASP* 3.1 36.3 + - - +
960A MET* 3.8 8.3 - - - +
961A VAL 3.3 0.4 - - - -
962A LEU* 1.3 76.3 - - - +
964A LYS* 1.3 59.8 + - - +
966A ALA* 2.9 26.9 + - + +
967A LYS* 3.2 24.1 + - + +
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Residues in contact with LYS 964 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727A THR* 4.9 2.2 - - + -
960A MET 3.4 9.6 + - - +
961A VAL* 3.3 13.4 + - + +
962A LEU 3.2 0.6 - - - -
963A ASN* 1.3 74.6 - - - +
965A MET* 1.3 66.1 + - - +
967A LYS* 3.2 29.4 + - - +
968A GLY 3.4 11.1 + - - +
971A GLU 6.0 1.3 - - - +
972A ILE* 5.8 9.0 - - + -
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Residues in contact with MET 965 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724A ASP* 2.6 62.8 - - - +
725A ILE* 4.5 3.4 - - - +
727A THR* 4.0 9.8 - - + +
728A GLY* 4.0 16.2 - - - +
731A ILE* 3.7 18.5 - - + +
961A VAL 3.3 3.4 + - - +
962A LEU* 3.0 16.2 + - + +
964A LYS* 1.3 78.9 - - - +
966A ALA* 1.3 58.5 + - - +
967A LYS 3.0 1.2 + - - -
968A GLY 3.5 6.6 + - - -
1006A VAL* 3.7 28.9 - - + -
1009A ILE* 3.9 42.2 - - + -
1010A LEU* 5.9 0.9 - - + +
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Residues in contact with ALA 966 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724A ASP* 3.8 10.9 - - - +
927A ARG* 5.9 1.1 - - - +
962A LEU 2.8 12.3 + - - +
963A ASN* 2.9 23.3 + - + +
965A MET* 1.3 77.7 - - - +
967A LYS* 1.3 58.8 + - + +
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Residues in contact with LYS 967 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808A ASP* 4.9 13.7 + - - -
809A HIS* 5.3 9.5 - - - +
963A ASN* 3.2 24.3 + - + +
964A LYS* 3.3 8.3 - - - +
965A MET 3.0 0.4 - - - -
966A ALA* 1.3 80.4 - - + +
968A GLY* 1.3 63.9 + - - +
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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) + - + + + + + -
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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