Contacts of the helix formed by residues 950 - 967 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F PRO* 4.4 13.5 - - - -
96F ILE* 4.3 10.2 - - - +
938F LEU* 3.6 24.0 + - - -
939F VAL* 4.5 1.6 - - - +
948F PRO 3.3 0.2 + - - -
949F PRO* 1.3 71.1 - - - +
951F LEU* 1.3 60.5 + - - +
952F GLU 3.5 1.9 - - - +
953F ASP* 3.5 3.6 + - - +
954F THR* 2.8 35.8 + - - -
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Residues in contact with LEU 951 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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908F THR* 4.1 20.9 - - + +
911F ARG* 3.3 41.7 - - + +
912F ILE* 3.8 35.4 - - + -
947F TYR* 4.5 4.3 - - + -
948F PRO* 3.1 45.1 + - + +
949F PRO 3.4 2.1 + - - +
950F GLY* 1.3 76.9 - - - +
952F GLU* 1.3 64.3 + - - +
954F THR* 3.2 5.6 + - - -
955F LEU* 2.9 25.3 + - - +
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Residues in contact with GLU 952 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754F MET* 3.3 52.3 - - + +
755F ASN* 3.4 4.7 + - - +
942F ASN* 3.0 32.2 + - + +
945F SER* 2.3 44.7 + - - +
946F GLU 4.3 0.3 + - - -
947F TYR* 3.9 11.1 - - + +
948F PRO 4.3 2.6 + - - -
950F GLY 3.5 0.8 - - - +
951F LEU* 1.3 79.0 - - - +
953F ASP* 1.3 65.3 + - - +
955F LEU* 3.3 0.9 + - - +
956F ILE* 2.9 42.6 + - + +
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Residues in contact with ASP 953 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F ILE* 3.9 9.4 - - + -
231F ARG* 2.7 29.4 + - - +
938F LEU 3.3 22.1 - - - +
939F VAL* 3.6 12.3 - - - +
940F LYS 3.1 2.1 + - - -
941F LEU* 3.0 34.7 + - + +
942F ASN 4.2 8.1 + - - +
950F GLY 3.5 2.6 + - - +
951F LEU 3.2 0.4 - - - -
952F GLU* 1.3 82.5 + - - +
954F THR* 1.3 65.3 + - - +
956F ILE* 3.9 5.6 - - - +
957F LEU* 3.0 30.8 + - - +
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Residues in contact with THR 954 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F PRO* 5.9 0.2 - - - +
95F ALA* 3.9 20.3 - - + +
96F ILE* 3.9 10.2 + - - +
99F ALA* 4.9 3.5 - - + +
904F PHE* 3.7 35.9 - - + -
908F THR* 4.0 16.8 - - + +
950F GLY* 2.8 23.1 + - - -
951F LEU* 3.6 4.7 - - - -
953F ASP* 1.3 77.4 - - - +
955F LEU* 1.3 63.0 + - - +
957F LEU* 3.3 10.5 + - - +
958F THR* 3.1 30.0 + - + +
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Residues in contact with LEU 955 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747F PRO* 5.4 1.3 - - + -
750F GLU* 3.7 19.5 - - + -
754F MET* 3.7 26.0 - - + -
905F GLN* 3.8 34.1 - - + +
908F THR* 4.2 13.6 - - + +
909F LEU* 3.8 21.3 - - + -
912F ILE* 3.7 19.1 - - + -
951F LEU 2.9 16.1 + - - +
952F GLU 3.8 3.6 - - - +
954F THR* 1.3 75.8 - - - +
956F ILE* 1.3 62.1 + - - +
958F THR* 2.5 23.0 + - - +
959F MET* 3.0 22.9 + - + +
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Residues in contact with ILE 956 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754F MET* 4.5 1.1 - - - -
755F ASN* 4.1 15.3 - - + +
756F ILE* 3.6 38.1 - - + -
941F LEU* 3.4 38.6 - - + +
952F GLU* 2.9 43.4 + - + +
953F ASP 4.0 0.4 - - - +
954F THR 3.3 0.2 - - - -
955F LEU* 1.3 75.9 - - - +
957F LEU* 1.3 57.9 + - - +
959F MET* 3.2 9.4 + - + +
960F LYS* 2.8 52.1 + - + +
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Residues in contact with LEU 957 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F ILE* 3.8 28.7 - - + +
99F ALA* 4.0 18.4 - - + -
100F SER* 3.5 26.9 - - - +
103F LEU* 3.9 28.2 - - + +
230F ILE* 4.2 24.5 - - + +
231F ARG* 4.7 7.4 - - + +
901F LEU* 4.4 4.8 - - - +
941F LEU* 4.8 5.2 - - + -
953F ASP 3.0 22.3 + - - +
954F THR* 3.6 5.4 - - - +
956F ILE* 1.3 76.8 - - - +
958F THR* 1.3 62.5 + - - +
960F LYS* 3.9 6.4 - - + +
961F GLY* 2.9 21.1 + - - -
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Residues in contact with THR 958 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F ALA* 5.1 1.8 - - + -
901F LEU* 3.9 38.8 - - + +
904F PHE* 4.1 15.9 - - + -
905F GLN* 3.1 32.3 + - - +
908F THR* 5.1 0.2 - - - +
954F THR* 3.1 18.5 + - + +
955F LEU* 2.5 24.2 + - - -
957F LEU* 1.3 74.8 - - - +
959F MET* 1.3 59.5 + - - +
961F GLY* 3.2 0.5 + - - -
962F ILE* 2.8 37.9 + - - +
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Residues in contact with MET 959 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179F THR* 4.6 4.0 - - + -
747F PRO* 4.9 9.9 - - + -
751F TYR* 4.4 22.7 - - - -
754F MET* 4.5 3.4 - - - -
756F ILE* 3.5 31.6 - - + -
779F PHE* 4.3 19.5 - - + -
783F GLN* 3.1 21.2 + - + +
905F GLN* 3.4 17.7 - - - +
955F LEU* 3.0 35.7 + - + +
956F ILE* 3.5 14.4 - - + +
958F THR* 1.3 81.5 + - - +
960F LYS* 1.3 62.8 + - + +
963F ALA* 3.0 26.3 + - - +
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Residues in contact with LYS 960 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F LEU* 4.6 9.0 - - + -
179F THR* 3.4 44.7 + - + +
180F GLN* 3.4 25.9 + - + +
229F GLU 5.0 0.4 + - - -
230F ILE* 3.0 29.7 + - + +
232F ARG 4.2 10.7 + - - -
756F ILE* 5.7 2.2 - - + -
941F LEU* 4.1 8.6 - - + +
956F ILE* 2.8 42.9 + - + +
957F LEU* 3.9 9.9 - - + +
959F MET* 1.3 71.6 - - + +
961F GLY* 1.3 58.5 + - - +
963F ALA* 3.6 1.9 - - - +
964F ALA* 2.9 29.9 + - - +
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Residues in contact with GLY 961 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F LEU* 3.5 25.3 - - - +
106F LEU* 3.4 11.5 - - - +
901F LEU* 3.6 19.5 - - - -
957F LEU 2.9 12.1 + - - -
958F THR 3.2 0.2 + - - -
960F LYS* 1.3 73.5 - - - +
962F ILE* 1.3 65.0 + - - +
964F ALA* 3.1 1.8 + - - +
965F GLY 2.9 19.6 + - - -
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Residues in contact with ILE 962 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782F THR 4.3 1.1 - - - +
783F GLN* 3.8 35.0 - - - +
785F ARG* 5.3 0.9 - - - -
898F ILE* 4.2 20.2 - - + +
901F LEU* 3.8 29.1 - - + +
902F ASN* 3.7 21.1 - - - +
905F GLN* 3.5 27.6 - - - +
958F THR 2.8 25.7 + - - +
961F GLY* 1.3 71.3 - - - -
963F ALA* 1.3 57.4 + - - +
965F GLY* 3.3 0.5 + - - -
966F MET* 2.9 48.9 + - + +
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Residues in contact with ALA 963 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177F HIS* 5.5 2.9 + - + -
178F PRO* 5.2 6.1 - - + -
179F THR* 3.6 25.8 - - + +
675F GLU* 5.1 4.2 - - - +
779F PHE* 4.1 6.5 - - + -
782F THR* 6.0 1.8 - - - -
783F GLN* 3.6 10.6 - - - +
959F MET 3.0 20.2 + - - +
960F LYS 3.6 4.3 - - - +
962F ILE* 1.3 77.6 - - - +
964F ALA* 1.3 61.6 + - - +
966F MET* 4.8 3.4 - - - -
967F GLN* 3.0 24.9 + - - +
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Residues in contact with ALA 964 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F LEU* 4.7 4.0 - - + -
106F LEU* 4.6 6.1 - - + -
107F ASN* 4.7 14.1 - - - +
110F ASN* 4.0 15.1 + - - +
177F HIS* 5.5 9.4 - - + -
179F THR* 5.1 0.6 + - - -
894F ARG* 5.5 0.2 + - - -
960F LYS 2.9 18.8 + - - +
961F GLY* 3.1 8.3 + - - +
963F ALA* 1.3 76.1 - - - +
965F GLY* 1.3 59.7 + - - +
967F GLN* 3.4 19.3 + - - +
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Residues in contact with GLY 965 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F LEU* 3.9 18.3 - - - +
110F ASN* 5.1 0.2 - - - -
835F LYS* 5.1 0.5 - - - -
894F ARG* 3.2 34.1 + - - -
898F ILE* 3.7 24.9 - - - +
961F GLY 2.9 10.9 + - - -
962F ILE 3.9 0.9 - - - -
964F ALA* 1.3 76.1 - - - +
966F MET* 1.3 62.5 + - - +
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Residues in contact with MET 966 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782F THR* 3.8 24.9 - - + +
785F ARG* 3.9 17.5 - - - +
787F HIS* 3.9 17.9 - - - -
835F LYS* 2.7 80.0 + - + +
895F ASN* 4.7 5.4 - - - +
898F ILE* 3.8 23.8 - - + -
962F ILE* 2.9 32.1 + - + +
963F ALA* 4.3 2.5 - - - +
965F GLY* 1.3 78.2 - - - +
967F GLN* 1.3 61.4 + - - +
968F ASN 3.6 1.4 - - - +
969F THR* 4.4 1.5 - - + +
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Residues in contact with GLN 967 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F ASN* 4.8 11.7 - - - +
675F GLU* 3.5 42.3 + - - +
676F VAL* 4.7 2.1 - - - +
678F GLU* 6.0 3.4 - - - +
679F PHE* 3.8 32.6 - - - +
782F THR* 5.3 2.3 - - - +
894F ARG* 4.2 13.2 - - - +
963F ALA 3.0 16.0 + - - +
964F ALA* 3.4 21.2 + - - +
966F MET* 1.3 81.5 - - - +
968F ASN* 1.3 65.9 + - - +
969F THR* 3.6 4.3 + - - +
1004F FLC 2.9 30.9 + - - +
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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