Contacts of the helix formed by residues 950 - 967 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G PRO* 4.3 16.9 - - - +
95G ALA* 6.2 0.9 - - - -
96G ILE* 4.5 16.2 - - - +
948G PRO 3.3 0.2 + - - -
949G PRO* 1.3 69.6 - - - +
951G LEU* 1.3 64.4 + - - +
952G GLU 3.3 1.8 - - - -
953G ASP* 3.0 10.5 + - - +
954G THR* 3.0 29.3 + - - +
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Residues in contact with LEU 951 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908G THR* 4.0 16.4 - - + +
911G ARG* 3.9 40.2 - - + +
912G ILE* 3.5 48.6 - - + +
947G TYR* 4.4 4.5 - - + -
948G PRO* 2.9 35.5 + - + +
949G PRO 4.6 4.5 - - - +
950G GLY* 1.3 77.4 - - - +
952G GLU* 1.3 63.5 + - - +
954G THR* 3.5 7.2 - - + +
955G LEU* 3.1 27.4 + - - +
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Residues in contact with GLU 952 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754G MET* 3.4 35.2 - - + +
912G ILE* 5.3 0.2 - - - -
946G GLU* 3.0 41.1 + - - +
947G TYR* 4.0 39.0 - - + +
948G PRO 4.4 0.2 + - - -
950G GLY 3.3 0.6 - - - -
951G LEU* 1.3 80.0 - - - +
953G ASP* 1.3 71.2 + - - +
955G LEU* 3.8 1.2 - - - +
956G ILE* 3.2 27.6 + - + +
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Residues in contact with ASP 953 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G ILE* 3.6 30.6 - - + +
230G ILE* 4.5 21.0 - - + +
950G GLY* 3.0 6.2 + - - +
952G GLU* 1.3 88.9 - - - +
954G THR* 1.3 58.1 + - - +
956G ILE* 2.9 25.6 + - - +
957G LEU* 2.9 24.3 + - + +
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Residues in contact with THR 954 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G ALA* 4.7 18.8 - - + -
96G ILE* 4.6 7.3 - - + +
99G ALA* 4.4 5.0 - - - +
904G PHE* 3.8 29.0 - - + -
908G THR* 3.9 13.3 + - + +
950G GLY* 3.0 21.9 + - - +
951G LEU* 3.5 17.7 - - + +
953G ASP* 1.3 75.0 - - - +
955G LEU* 1.3 63.7 + - - +
957G LEU* 4.0 11.3 - - - +
958G THR* 2.9 29.9 + - - -
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Residues in contact with LEU 955 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747G PRO* 5.7 0.9 - - + -
750G GLU* 3.9 28.9 - - + -
754G MET* 4.1 12.1 - - - -
905G GLN* 4.1 17.9 - - + +
908G THR* 3.9 25.8 - - + -
909G LEU* 4.0 23.1 - - + +
912G ILE* 3.6 21.3 - - + -
951G LEU 3.1 20.8 + - - +
952G GLU* 3.8 4.5 - - - +
954G THR* 1.3 79.7 - - - +
956G ILE* 1.3 58.0 + - - +
958G THR* 3.1 10.4 - - - -
959G MET* 3.0 33.5 - - + +
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Residues in contact with ILE 956 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230G ILE* 3.8 24.2 - - + -
231G ARG* 5.4 5.6 - - + -
754G MET* 3.4 32.1 - - + +
756G ILE* 4.0 29.2 - - + -
952G GLU* 3.2 12.1 + - + +
953G ASP* 2.9 12.8 + - - +
955G LEU* 1.3 72.6 - - - +
957G LEU* 1.3 62.1 + - - +
958G THR 3.0 1.3 - - - -
959G MET* 2.8 25.8 + - + +
960G LYS* 2.9 24.4 + - + +
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Residues in contact with LEU 957 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G ILE* 3.8 39.3 - - + +
99G ALA* 3.9 21.8 - - + +
100G SER* 4.4 13.9 - - - +
103G LEU* 4.1 26.1 - - + +
228G ASP* 4.8 5.2 - - - +
230G ILE* 3.8 32.1 - - + -
231G ARG* 5.6 1.6 - - - +
901G LEU* 4.4 6.8 - - - +
953G ASP* 2.9 25.2 + - + +
954G THR* 4.1 2.2 - - - +
956G ILE* 1.3 75.7 - - - +
958G THR* 1.3 63.4 + - - +
960G LYS* 4.0 6.4 - - + +
961G GLY* 3.0 21.3 + - - -
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Residues in contact with THR 958 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G ALA* 5.1 0.9 - - - +
901G LEU* 3.9 16.5 + - - +
904G PHE* 4.3 8.3 - - - +
905G GLN* 3.1 63.5 + - + +
908G THR* 5.0 0.7 + - - -
954G THR* 2.9 20.4 + - - -
955G LEU* 3.1 14.6 - - - +
957G LEU* 1.3 79.3 - - - +
959G MET* 1.3 55.7 + - - +
961G GLY* 3.9 0.5 - - - -
962G ILE* 3.0 36.0 + - + +
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Residues in contact with MET 959 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179G THR* 4.3 5.4 - - - +
747G PRO* 4.6 13.9 - - - -
750G GLU* 5.3 0.2 - - + -
751G TYR* 4.4 24.2 - - + +
754G MET* 4.5 19.3 - - - -
756G ILE* 4.6 15.9 - - + -
779G PHE* 4.1 27.8 - - + -
783G GLN* 3.4 13.5 + - - +
905G GLN* 3.6 19.7 - - - +
955G LEU* 3.0 25.6 - - + +
956G ILE* 2.8 19.6 + - + +
958G THR* 1.3 69.1 - - - +
960G LYS* 1.3 59.7 + - - +
963G ALA* 2.9 33.3 + - - +
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Residues in contact with LYS 960 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G LEU* 4.5 17.6 - - + +
179G THR* 3.0 44.6 + - + +
180G GLN* 2.5 39.1 + - + +
181G SER 4.2 2.1 - - - +
230G ILE* 4.8 4.5 - - + -
231G ARG* 4.0 41.3 - - - +
956G ILE* 2.9 26.5 + - + +
957G LEU* 4.0 6.3 - - + +
959G MET* 1.3 76.7 - - - +
961G GLY* 1.3 57.9 + - - +
963G ALA* 3.8 1.6 - - - +
964G ALA* 2.9 30.7 + - - +
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Residues in contact with GLY 961 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G LEU* 3.6 22.8 - - - +
106G LEU* 3.3 12.3 - - - +
901G LEU* 3.6 21.5 - - - -
957G LEU 3.0 11.8 + - - -
960G LYS* 1.3 75.1 - - - +
962G ILE* 1.3 65.7 + - - +
964G ALA* 3.2 1.7 + - - +
965G GLY 3.0 19.1 + - - -
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Residues in contact with ILE 962 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782G THR 4.3 1.3 - - - +
783G GLN* 3.7 40.6 - - - +
898G ILE* 4.3 21.0 - - + +
901G LEU* 3.9 22.0 - - + +
902G ASN* 3.7 21.3 - - - +
905G GLN* 3.9 6.5 - - - +
958G THR* 3.0 38.4 + - + +
961G GLY* 1.3 74.8 - - - +
963G ALA* 1.3 64.9 + - - +
965G GLY* 3.1 2.1 + - - -
966G MET* 2.9 42.6 + - + +
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Residues in contact with ALA 963 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177G HIS* 5.4 3.9 + - - +
178G PRO* 6.0 1.8 - - + -
179G THR* 3.7 26.2 - - + -
675G GLU* 5.3 2.6 - - - +
779G PHE* 4.1 11.2 - - + -
783G GLN* 3.6 12.8 - - - +
959G MET 2.9 17.7 + - - +
960G LYS 3.8 0.2 - - - +
962G ILE* 1.3 76.8 - - - +
964G ALA* 1.3 56.1 + - - +
966G MET* 4.7 3.6 - - - -
967G GLN* 2.9 32.1 + - - +
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Residues in contact with ALA 964 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G LEU* 4.7 9.9 - - + -
106G LEU* 4.8 3.6 - - + -
107G ASN* 4.7 9.4 - - - +
110G ASN* 3.7 19.8 + - - +
177G HIS* 5.6 9.9 - - + -
179G THR* 5.2 0.4 - - - +
960G LYS 2.9 21.1 + - - +
961G GLY* 3.2 8.0 + - - +
963G ALA* 1.3 76.3 - - - +
965G GLY* 1.3 60.1 + - - +
967G GLN* 3.4 17.8 + - - +
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Residues in contact with GLY 965 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G LEU* 4.1 8.7 - - - +
110G ASN* 5.0 1.8 - - - -
835G LYS* 5.0 1.6 - - - +
891G LEU* 5.4 0.2 - - - +
894G ARG* 3.0 36.6 + - - -
898G ILE* 3.6 27.1 - - - +
961G GLY 3.0 13.3 + - - -
962G ILE 3.1 1.1 + - - -
964G ALA* 1.3 79.5 - - - +
966G MET* 1.3 57.2 + - - +
967G GLN 3.5 0.2 - - - -
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Residues in contact with MET 966 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782G THR* 3.1 31.6 - - - +
785G ARG* 3.3 28.5 - - - -
787G HIS* 3.3 28.5 - - + +
835G LYS* 2.6 56.6 + - - +
895G ASN* 6.1 0.4 - - - +
898G ILE* 4.7 9.9 - - + -
962G ILE* 2.9 30.4 + - + +
963G ALA* 4.1 4.3 - - - +
965G GLY* 1.3 78.8 - - - +
967G GLN* 1.3 65.7 + - - +
968G ASN 3.6 1.6 - - - +
969G THR* 4.2 9.1 - - + +
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Residues in contact with GLN 967 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G ASN* 4.2 12.1 + - - +
675G GLU* 3.1 43.8 - - - +
676G VAL* 4.6 1.4 - - - +
679G PHE* 4.0 26.2 - - - +
894G ARG* 3.3 37.1 - - - +
963G ALA 2.9 15.4 + - - +
964G ALA* 3.4 19.7 + - - +
966G MET* 1.3 81.9 - - - +
968G ASN* 1.3 69.7 + - - +
969G THR* 3.6 5.2 + - - +
1001G GOL 4.2 11.2 - - - +
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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