Contacts of the helix formed by residues 960 - 969 (chain B) in PDB entry 6RQT
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 ILE 960 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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833A LEU* 4.6 9.4 - - + -
943A ILE* 3.9 27.8 - - + -
985A ARG* 4.2 9.2 - - - +
986A PHE* 3.2 30.3 - - + +
987A TYR* 3.8 25.8 - - + +
709B PHE* 3.3 30.3 + - + +
954B PHE* 6.4 0.2 - - + -
958B MET* 3.9 8.5 - - + -
959B THR* 1.3 74.8 - - - +
961B GLY* 1.3 60.4 + - - +
962B MET 3.2 2.2 - - - -
963B PHE* 3.3 23.0 + - + +
964B VAL* 3.0 29.0 + - + +
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Residues in contact with GLY 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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706B PHE* 4.4 10.5 - - - -
709B PHE* 3.3 18.4 + - - -
710B ASN* 3.6 9.2 + - - -
921B HIS* 3.5 10.3 - - - -
959B THR 3.4 1.0 - - - -
960B ILE* 1.3 78.4 - - - +
962B MET* 1.3 55.8 + - - +
964B VAL* 3.1 11.1 + - - +
965B GLU* 2.8 34.8 + - - +
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Residues in contact with MET 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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773B VAL* 5.7 6.1 - - + -
775B VAL* 5.2 5.3 - - + +
919B SER* 3.2 33.2 - - - -
921B HIS* 3.2 25.8 + - + +
923B GLN* 3.7 16.6 - - + -
949B ILE* 3.7 27.8 - - + -
953B ALA* 5.9 2.7 - - + -
954B PHE* 3.6 35.7 - - + -
959B THR* 4.1 11.5 + - - +
960B ILE 3.2 0.6 - - - -
961B GLY* 1.3 72.1 - - - +
963B PHE* 1.3 65.6 + - - +
965B GLU* 4.6 0.7 - - - +
966B SER* 3.5 19.5 + - - +
1027B TYR* 4.7 1.6 - - - -
1031B VAL* 4.6 11.6 - - + +
1033B TYR* 5.4 0.7 - - - -
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Residues in contact with PHE 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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828A CYS* 3.5 22.0 - - + -
829A GLY* 3.6 34.5 - - - -
830A MET* 4.8 10.5 - - - -
833A LEU* 4.2 18.2 - - + -
925A MET* 6.0 0.9 - - + -
943A ILE* 5.6 2.9 - - + -
775B VAL* 4.8 5.6 - - + -
954B PHE* 3.4 53.3 - + + -
959B THR 3.8 4.4 + - - -
960B ILE* 3.3 37.2 + - + +
962B MET* 1.3 79.3 - - - +
964B VAL* 1.3 61.8 + - + +
965B GLU 3.2 1.2 + - - -
966B SER 3.3 0.3 + - - -
967B LEU* 4.0 1.5 - - - +
1027B TYR* 2.2 42.6 + + + -
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Residues in contact with VAL 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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830A MET* 4.1 25.1 - - + -
987A TYR* 5.6 1.1 - - + -
706B PHE* 3.6 26.9 - - + -
709B PHE* 4.0 9.4 - - + -
960B ILE* 3.0 19.3 + - + +
961B GLY* 3.1 11.6 + - - +
963B PHE* 1.3 78.5 - - + +
965B GLU* 1.3 60.8 + - - +
966B SER 3.4 0.2 - - - -
967B LEU* 3.3 26.6 - - + +
968B ALA 3.8 1.7 + - - -
992B PRO* 3.7 37.5 - - + +
996B PHE* 4.1 7.1 - - - -
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Residues in contact with GLU 965 (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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705B PRO* 5.5 1.3 - - + -
706B PHE* 3.1 42.4 - - + -
752B VAL* 3.3 38.0 - - + +
921B HIS* 3.6 23.6 - - + +
961B GLY 2.8 17.3 + - - +
964B VAL* 1.3 76.2 - - - +
966B SER* 1.3 59.6 + - - +
967B LEU 3.2 1.3 - - - -
968B ALA* 3.0 36.5 + - - +
969B GLY 3.7 4.0 + - - -
996B PHE* 3.4 16.8 - - - -
1030B VAL 3.9 3.1 - - - +
1031B VAL* 3.5 12.7 - - + +
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Residues in contact with SER 966 (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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773B VAL* 4.4 13.4 - - - +
775B VAL* 5.0 0.7 - - - +
962B MET* 3.5 9.3 + - - +
963B PHE 3.3 3.7 + - - -
965B GLU* 1.3 73.8 - - - +
967B LEU* 1.3 64.0 + - - +
968B ALA 3.2 0.2 - - - -
969B GLY 4.1 3.2 + - - -
970B LYS* 4.6 2.9 + - - +
1027B TYR* 3.2 26.8 - - - -
1028B VAL 3.5 3.6 - - - +
1029B GLY* 3.2 33.5 - - - -
1030B VAL 3.9 9.3 + - - +
1031B VAL* 3.3 21.7 - - - +
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Residues in contact with LEU 967 (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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830A MET* 3.8 30.3 - - + -
963B PHE 4.0 5.4 - - - +
964B VAL* 3.3 15.0 + - + +
965B GLU 3.2 1.0 - - - -
966B SER* 1.3 76.7 - - - +
968B ALA* 1.3 58.0 + - - +
970B LYS* 3.0 30.4 + - + +
971B ALA 3.7 1.9 + - - -
992B PRO 5.3 4.0 - - - +
993B ALA* 6.0 2.0 - - - -
996B PHE* 4.6 16.6 - - + +
1000B LEU* 4.0 20.2 - - + +
1007B TYR 4.3 7.0 - - - +
1008B HIS 3.7 5.4 - - - +
1009B GLY* 3.7 30.7 - - - +
1027B TYR* 3.0 40.5 + - + +
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Residues in contact with ALA 968 (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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965B GLU* 3.0 34.4 + - - +
967B LEU* 1.3 78.4 - - - +
969B GLY* 1.3 51.5 + - - +
970B LYS 3.2 0.2 - - - -
971B ALA* 2.9 5.5 + - - +
972B GLY 2.6 20.3 + - - -
979B GLN* 2.5 39.2 + - - +
996B PHE* 3.6 28.5 - - + -
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Residues in contact with GLY 969 (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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751B ILE* 5.9 2.7 - - - -
965B GLU 3.7 6.5 + - - -
966B SER 4.1 2.2 + - - -
967B LEU 3.1 1.2 + - - -
968B ALA* 1.3 76.3 - - - +
970B LYS* 1.3 60.0 + - - +
972B GLY 4.0 1.6 - - - -
973B ALA* 2.7 32.1 + - - +
974B LEU* 3.2 6.4 + - - +
979B GLN* 3.9 3.3 - - - +
1030B VAL* 3.6 31.9 + - - +
44J TYR* 5.1 3.4 - - - -
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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
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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