Contacts of the helix formed by residues 950 - 967 (chain B) in PDB entry 6V3O
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 950 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B PRO* 4.3 10.5 - - - -
96B ILE* 4.2 10.5 - - - +
938B LEU* 3.6 26.0 + - - -
939B VAL* 4.4 1.2 - - - +
948B PRO 3.2 0.6 + - - -
949B PRO* 1.3 71.8 - - - +
951B LEU* 1.3 56.0 + - - +
952B GLU* 3.5 2.1 - - - +
953B ASP* 3.6 4.1 + - - +
954B THR* 2.5 39.4 + - - -
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Residues in contact with LEU 951 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908B THR* 3.5 29.9 - - + +
911B ARG* 4.0 38.6 - - + +
912B ILE* 3.9 28.0 - - + -
947B TYR* 4.9 4.0 - - + -
948B PRO* 3.2 41.2 + - + +
949B PRO 3.4 2.2 - - - +
950B GLY* 1.3 75.6 - - - +
952B GLU* 1.3 60.5 + - - +
954B THR* 3.1 4.5 + - - -
955B LEU* 2.8 32.7 + - - +
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Residues in contact with GLU 952 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754B MET* 3.7 38.0 - - + +
755B ASN* 3.4 23.6 + - - +
942B ASN* 3.1 33.3 + - + +
945B SER* 2.3 39.1 + - - +
946B GLU 4.3 0.7 + - - -
947B TYR* 3.9 16.0 - - + +
948B PRO 4.3 3.6 + - - +
950B GLY 4.7 0.6 - - - +
951B LEU* 1.3 77.5 - - - +
953B ASP* 1.3 63.0 + - - +
955B LEU* 3.5 0.7 + - - +
956B ILE* 3.0 42.4 + - + +
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Residues in contact with ASP 953 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ILE* 3.9 9.2 - - + -
231B ARG* 2.9 21.3 + - - +
938B LEU 3.2 25.1 - - - +
939B VAL* 3.4 13.2 - - - +
940B LYS 3.4 0.5 + - - -
941B LEU* 2.8 48.7 + - + +
942B ASN 4.4 5.0 + - - +
945B SER* 5.2 0.5 + - - -
950B GLY 3.6 3.1 + - - +
951B LEU 3.2 0.2 - - - -
952B GLU* 1.3 83.6 - - - +
954B THR* 1.3 62.4 + - - +
956B ILE 3.7 0.2 + - - -
957B LEU* 3.1 31.8 + - - +
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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
----------------------------------------------------------
95B ALA* 4.0 15.1 - - + +
96B ILE* 3.8 13.9 + - - +
99B ALA* 4.9 2.9 - - + -
904B PHE* 3.7 36.8 - - + -
908B THR* 4.0 15.3 - - + +
950B GLY 2.5 25.6 + - - -
951B LEU* 3.6 6.7 - - - -
953B ASP* 1.3 76.2 - - - +
955B LEU* 1.3 61.8 + - - +
957B LEU* 3.3 11.1 + - - +
958B THR* 3.1 25.7 + - + +
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Residues in contact with LEU 955 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747B PRO* 5.4 2.2 - - + -
750B GLU* 3.6 23.6 - - + -
754B MET* 3.6 28.5 - - + -
905B GLN* 3.7 34.8 - - + +
908B THR* 4.3 12.7 - - + +
909B LEU* 3.8 20.4 - - + +
912B ILE* 3.7 12.8 - - + -
951B LEU 2.8 16.3 + - - +
952B GLU 3.9 3.6 - - - +
954B THR* 1.3 75.0 - - - +
956B ILE* 1.3 64.3 + - - +
958B THR* 2.7 20.4 + - - +
959B MET* 3.0 22.9 + - + +
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Residues in contact with ILE 956 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754B MET* 4.2 7.0 - - + -
755B ASN* 3.9 25.1 - - + +
756B ILE* 4.4 13.2 - - + -
941B LEU* 3.8 31.6 - - + +
952B GLU* 3.0 41.9 + - + +
953B ASP 4.0 3.1 - - - +
955B LEU* 1.3 75.5 - - - +
957B LEU* 1.3 57.6 + - - +
959B MET* 3.2 22.1 + - + +
960B LYS* 2.8 53.7 + - - +
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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
----------------------------------------------------------
96B ILE* 3.8 41.3 - - + +
99B ALA* 3.9 18.8 - - + -
100B SER* 4.0 15.5 - - - +
103B LEU* 4.2 12.0 - - + +
230B ILE* 3.3 33.2 - - + -
231B ARG* 4.9 8.7 - - + +
901B LEU* 4.5 3.8 - - - +
941B LEU* 4.6 7.6 - - + -
953B ASP 3.1 26.9 + - - +
954B THR* 3.5 6.3 - - - +
955B LEU 3.2 0.2 - - - -
956B ILE* 1.3 76.7 - - - +
958B THR* 1.3 63.1 + - - +
960B LYS* 3.2 5.1 + - + +
961B GLY* 2.9 21.3 + - - -
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Residues in contact with THR 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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99B ALA* 5.2 1.1 - - + -
901B LEU* 3.8 40.8 - - + +
904B PHE* 4.0 22.7 - - + -
905B GLN* 3.0 28.5 + - - +
908B THR* 5.3 0.4 - - - +
954B THR* 3.1 18.7 + - + +
955B LEU* 2.7 21.2 + - - -
957B LEU* 1.3 75.4 - - + +
959B MET* 1.3 57.5 + - - +
961B GLY 3.3 0.3 + - - -
962B ILE* 2.8 37.8 + - - +
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Residues in contact with MET 959 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B THR* 4.4 2.4 - - - +
747B PRO* 5.0 9.6 - - + -
751B TYR* 4.1 35.4 - - - -
754B MET* 4.4 13.0 - - - -
756B ILE* 4.0 21.1 - - + -
779B PHE* 4.1 11.2 - - + -
783B GLN* 3.3 18.6 + - + +
905B GLN* 3.4 15.9 - - - +
955B LEU* 3.0 18.2 + - + +
956B ILE* 3.5 36.3 - - + +
958B THR* 1.3 81.6 + - - +
960B LYS* 1.3 61.5 + - - +
963B ALA* 3.0 26.0 + - - +
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Residues in contact with LYS 960 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 4.2 9.2 - - + -
177B HIS* 6.0 0.2 - - - -
179B THR* 3.5 40.3 + - - +
180B GLN* 3.1 31.4 + - + +
230B ILE* 3.0 37.4 + - + +
232B ARG 4.4 6.7 + - - -
756B ILE* 4.6 2.9 - - + -
941B LEU* 4.0 10.6 - - - +
956B ILE* 2.8 43.8 + - + +
957B LEU* 3.6 5.4 - - - +
959B MET* 1.3 73.3 - - - +
961B GLY* 1.3 58.3 + - - +
963B ALA* 3.6 2.4 - - - +
964B ALA* 2.9 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
----------------------------------------------------------
103B LEU* 3.5 25.5 - - - +
106B LEU* 3.2 10.9 - - - +
898B ILE* 4.9 0.7 - - - +
901B LEU* 3.7 19.7 - - - -
957B LEU 2.9 11.8 + - - -
960B LYS* 1.3 74.2 - - - +
962B ILE* 1.3 60.6 + - - +
964B ALA* 3.1 0.6 + - - -
965B GLY* 2.9 25.1 + - - -
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Residues in contact with ILE 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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782B THR 4.3 0.2 - - - +
783B GLN* 3.7 35.7 - - - +
785B ARG* 5.3 0.9 - - - -
898B ILE* 4.3 19.5 - - + +
901B LEU* 3.8 30.9 - - + +
902B ASN* 3.6 21.8 - - - +
905B GLN* 3.7 24.7 - - - +
958B THR 2.8 23.9 + - - +
961B GLY* 1.3 71.0 - - - -
963B ALA* 1.3 58.8 + - - +
965B GLY* 3.3 0.9 + - - -
966B MET* 2.9 48.4 + - + +
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Residues in contact with ALA 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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177B HIS* 5.4 4.7 + - + -
178B PRO* 5.3 5.4 - - + -
179B THR* 3.6 25.4 - - + +
675B GLU* 5.1 4.2 - - - +
779B PHE* 4.3 5.4 - - + -
783B GLN* 3.6 11.5 - - - +
959B MET 3.0 18.6 + - - +
960B LYS 3.6 4.3 - - - +
962B ILE* 1.3 77.4 - - - +
964B ALA* 1.3 61.6 + - - +
966B MET* 4.7 3.4 - - - -
967B GLN* 3.1 24.1 + - - +
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Residues in contact with ALA 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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103B LEU* 4.5 8.1 - - + -
106B LEU* 4.3 9.2 - - + -
107B ASN* 4.6 9.4 - - - +
110B ASN* 4.0 10.3 + - - +
177B HIS* 5.7 8.7 - - + -
179B THR* 5.2 0.4 + - - -
960B LYS 2.9 18.0 + - - +
961B GLY* 3.1 8.5 + - - +
963B ALA* 1.3 76.5 - - - +
965B GLY* 1.3 61.5 + - - +
967B GLN* 3.4 23.0 + - - +
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Residues in contact with GLY 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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106B LEU* 3.7 16.1 - - - +
110B ASN* 5.2 0.4 - - - -
835B LYS* 5.1 0.9 - - - -
894B ARG* 3.1 35.2 + - - -
898B ILE* 3.6 25.3 - - - +
961B GLY 2.9 13.9 + - - -
962B ILE 3.8 0.2 - - - -
964B ALA* 1.3 79.3 - - - +
966B MET* 1.3 56.4 + - - +
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Residues in contact with MET 966 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782B THR* 4.2 12.6 - - + +
785B ARG* 3.9 18.6 - - - -
787B HIS* 3.0 28.9 - - - +
835B LYS* 2.7 79.1 + - + +
898B ILE* 4.8 10.8 - - + -
962B ILE* 2.9 34.7 + - + +
963B ALA* 4.3 3.4 - - - +
965B GLY* 1.3 77.2 - - - +
967B GLN* 1.3 63.7 + - - +
968B ASN 3.7 1.2 - - - +
969B THR* 3.6 11.0 - - + -
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Residues in contact with GLN 967 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASN* 4.5 12.7 + - - +
675B GLU* 3.3 41.1 - - - +
676B VAL* 4.1 5.0 - - - +
679B PHE* 3.9 26.5 - - - +
894B ARG* 3.6 25.7 - - - +
963B ALA 3.1 13.8 + - - +
964B ALA* 3.4 20.6 + - - +
965B GLY 4.6 0.2 - - - +
966B MET* 1.3 82.1 - - - +
968B ASN* 1.3 62.5 + - - +
969B THR* 3.7 5.7 + - - +
1004B FLC 3.3 25.3 - - - +
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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