Contacts of the helix formed by residues 949 - 964 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779B VAL* 3.6 26.5 - - + -
945B CYS* 3.6 2.0 - - - -
947B ASP* 2.4 35.6 + - - +
948B GLY* 1.3 69.8 - - - +
950B GLY* 1.3 60.0 + - - +
951B ARG 3.6 0.4 - - - -
953B GLY* 2.9 23.2 + - - -
985B ARG* 4.9 0.2 - - - +
986B PRO 3.9 1.8 - - - +
987B GLY 3.3 22.2 - - - +
988B MET* 3.4 5.9 - - - +
989B VAL 2.9 12.3 + - - -
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Residues in contact with GLY 950 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947B ASP* 3.1 10.5 + - - -
949B ALA* 1.3 83.6 - - - +
951B ARG* 1.3 52.7 + - - +
954B THR* 2.7 31.4 + - - -
989B VAL* 3.5 2.9 - - - -
990B GLN* 3.6 21.1 - - - -
994B GLN* 3.4 21.6 - - - +
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Residues in contact with ARG 951 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845B LEU* 3.3 25.2 + - + +
846B THR* 3.3 21.6 + - - +
850B GLU* 3.2 14.5 + - - -
855B GLN* 3.3 24.2 + - - -
911B TRP* 2.7 76.7 + - + +
912B TYR 3.8 4.0 - - - -
913B ASP* 3.7 20.8 + - - +
914B ARG 4.6 1.3 - - - +
945B CYS* 4.1 16.7 - - + +
946B SER* 3.4 22.8 - - - +
950B GLY* 1.3 71.6 - - - +
952B SER* 1.3 60.6 + - - +
954B THR* 3.1 2.8 + - - -
955B TYR 2.8 26.3 + - - -
994B GLN* 4.0 9.9 - - - +
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Residues in contact with SER 952 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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818B ALA* 5.1 5.2 - - - -
845B LEU* 3.5 9.4 - - - +
943B VAL* 3.6 15.7 - - - +
944B HIS* 3.2 25.6 + - - -
945B CYS* 3.1 17.9 + - - -
948B GLY* 3.6 24.2 - - - -
949B ALA 4.0 0.2 + - - -
950B GLY 3.5 0.2 - - - -
951B ARG* 1.3 79.7 - - - +
953B GLY* 1.3 56.3 + - - +
955B TYR* 3.2 2.6 + - - +
956B VAL* 2.9 33.7 + - - +
988B MET* 5.0 0.4 - - - -
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Residues in contact with GLY 953 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949B ALA 2.9 23.5 + - - -
952B SER* 1.3 69.7 - - - +
954B THR* 1.3 59.9 + - - +
956B VAL* 3.8 1.6 - - - -
957B LEU* 3.0 23.4 + - - +
981B LEU* 3.9 3.5 - - - +
988B MET* 3.6 28.3 - - - -
989B VAL* 3.2 19.7 - - - +
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Residues in contact with THR 954 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911B TRP* 3.5 24.9 - - + -
950B GLY 2.7 22.4 + - - -
951B ARG 3.1 6.1 + - - -
953B GLY* 1.3 75.6 - - - +
955B TYR* 1.3 64.0 + - - +
957B LEU* 3.4 3.5 + - - +
958B ILE* 3.2 25.5 + - + +
989B VAL* 3.7 12.7 - - - +
994B GLN* 3.5 37.5 - - + +
997B PHE* 4.1 13.2 - - + -
998B ALA* 4.2 8.1 - - + -
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Residues in contact with TYR 955 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816B TYR* 4.8 3.8 - + - -
843B VAL* 4.4 19.5 - - + -
845B LEU* 3.6 32.1 - - + -
911B TRP* 3.8 6.2 - - + -
923B LEU* 4.4 17.0 - - + -
926B PHE* 3.8 23.3 - + - -
927B ARG* 3.8 28.1 - - + +
930B VAL* 3.4 28.7 - - + +
931B ASN* 4.6 0.3 + - - -
941B ILE* 5.8 1.1 - - + -
943B VAL* 4.5 14.1 - - + -
951B ARG 2.8 6.8 + - - +
952B SER* 3.5 7.4 - - - +
954B THR* 1.3 76.0 - - - +
956B VAL* 1.3 66.6 + - + +
958B ILE* 3.1 9.5 + - + +
959B ASP* 3.0 41.5 + - + +
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Residues in contact with VAL 956 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806B ILE* 4.7 3.4 - - + -
816B TYR* 3.8 44.6 - - + -
818B ALA* 5.3 4.3 - - + -
943B VAL* 4.5 15.0 - - + -
952B SER* 2.9 25.2 + - - +
953B GLY* 4.1 5.8 - - - +
955B TYR* 1.3 75.7 - - + +
957B LEU* 1.3 68.5 + - - +
958B ILE 3.1 0.2 + - - -
959B ASP* 3.2 4.0 + - - +
960B MET* 2.8 28.9 + - + +
981B LEU* 3.8 26.7 - - + -
988B MET* 4.4 11.4 - - + -
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Residues in contact with LEU 957 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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953B GLY 3.0 20.2 + - - +
954B THR 3.7 4.9 - - - +
955B TYR 3.4 0.2 - - - -
956B VAL* 1.3 75.2 - - - +
958B ILE* 1.3 56.9 + - - +
960B MET* 3.7 2.8 - - - +
961B VAL* 3.0 35.1 + - + +
974B ILE* 3.6 43.3 - - + +
977B THR* 3.8 13.7 - - + -
978B LEU* 3.8 30.7 - - + +
981B LEU* 3.7 9.4 - - + +
989B VAL* 4.1 16.6 - - + -
995B PHE* 4.3 8.3 - - + -
998B ALA* 4.1 20.6 - - + -
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Residues in contact with ILE 958 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923B LEU* 4.1 15.3 - - + -
924B LEU* 4.5 11.4 - - + -
927B ARG* 4.6 6.1 - - - -
954B THR* 3.2 17.5 + - + +
955B TYR* 3.1 8.6 + - + +
956B VAL 3.1 1.0 - - - -
957B LEU* 1.3 76.0 - - - +
959B ASP* 1.3 68.4 + - - +
961B VAL* 3.3 1.6 + - - +
962B LEU* 3.0 45.1 + - + +
997B PHE* 4.1 15.3 - - + -
998B ALA* 3.6 33.4 - - + +
1001B ALA* 3.6 22.7 - - + -
1002B VAL* 4.4 10.5 - - + -
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Residues in contact with ASP 959 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816B TYR* 2.7 32.8 + - + +
927B ARG* 2.9 30.1 + - - +
931B ASN* 3.1 25.5 + - - +
941B ILE* 4.6 3.8 - - - +
955B TYR* 3.0 33.9 + - + +
956B VAL 3.9 1.3 - - - +
958B ILE* 1.3 77.2 - - - +
960B MET* 1.3 57.5 + - - +
962B LEU* 3.5 0.3 + - - +
963B ASN* 2.9 38.0 + - - +
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Residues in contact with MET 960 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806B ILE* 5.2 0.9 - - - -
807B MET 4.9 5.2 - - - +
808B ASP* 4.7 20.6 - - + -
816B TYR* 3.9 22.2 + - + +
956B VAL* 2.8 19.2 + - - +
957B LEU 3.7 4.5 - - - +
959B ASP* 1.3 74.8 - - - +
961B VAL* 1.3 67.7 + - - +
963B ASN* 3.5 5.6 + - - +
964B LYS* 3.3 19.1 + - - +
977B THR* 3.5 25.8 - - + -
980B HIS* 4.1 19.7 - - + -
981B LEU* 3.4 32.1 - - - -
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Residues in contact with VAL 961 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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957B LEU* 3.0 28.5 + - + +
958B ILE 3.3 2.9 + - - +
960B MET* 1.3 75.2 - - - +
962B LEU* 1.3 59.5 + - - +
964B LYS* 3.0 21.4 + - - +
965B MET* 3.3 9.2 + - + +
972B ILE* 4.8 11.7 - - + -
974B ILE* 3.8 49.8 - - + -
977B THR* 4.4 12.8 - - + +
1002B VAL* 4.1 20.9 - - + -
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Residues in contact with LEU 962 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924B LEU* 4.0 16.6 - - + -
927B ARG* 3.5 38.1 + - - +
958B ILE* 3.0 34.9 + - + +
961B VAL* 1.3 78.1 - - - +
963B ASN* 1.3 58.1 + - - +
965B MET* 2.9 30.4 + - + +
966B ALA* 3.2 11.1 + - - +
1002B VAL* 4.1 27.4 - - + +
1005B GLU* 3.8 26.7 - - + -
1006B VAL* 4.7 8.1 - - + -
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Residues in contact with ASN 963 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816B TYR* 4.1 4.8 + - - -
927B ARG* 3.0 21.5 + - - -
931B ASN* 3.9 7.7 + - - +
959B ASP* 2.9 42.8 + - - +
960B MET* 3.9 6.2 - - - +
962B LEU* 1.3 75.4 - - - +
964B LYS* 1.3 57.0 + - - +
965B MET 3.4 1.3 + - - -
966B ALA* 3.8 17.6 + - - +
967B LYS* 4.0 9.2 + - - +
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Residues in contact with LYS 964 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727B THR* 4.5 2.9 - - - +
960B MET 3.3 10.2 + - - +
961B VAL* 3.0 13.6 + - - +
963B ASN* 1.3 74.8 - - - +
965B MET* 1.3 59.6 + - - +
966B ALA 3.6 0.2 - - - -
967B LYS* 4.2 8.4 - - + +
968B GLY 4.1 16.5 + - - +
972B ILE* 5.7 3.8 - - - +
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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
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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