Contacts of the helix formed by residues 884 - 893 (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 ASP 884 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135F GLY 4.6 4.7 - - - +
136F SER* 3.9 30.3 + - - -
651F PRO* 5.8 1.7 - - - +
881F LEU* 2.9 30.6 + - + +
883F GLY* 1.3 80.1 - - - +
885F PRO* 1.3 64.0 - - - +
886F PHE* 3.7 7.0 + - - +
887F LEU* 3.1 35.6 + - - +
888F LYS* 3.1 18.0 + - - +
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Residues in contact with PRO 885 (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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28F VAL* 4.2 16.7 - - + +
881F LEU 3.9 2.0 - - - +
882F GLU 4.2 7.9 - - - +
883F GLY 3.6 7.4 - - - +
884F ASP* 1.3 88.3 - - - +
886F PHE* 1.3 74.8 + - + +
888F LYS* 3.7 8.8 - - + +
889F GLN* 2.9 31.2 + - - +
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Residues in contact with PHE 886 (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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28F VAL* 3.4 49.6 - - + -
29F SER* 4.3 8.5 - - - -
120F ARG* 3.6 37.4 + - - +
126F LEU* 4.5 26.0 - - + -
136F SER* 5.0 2.0 - - - +
138F THR* 3.5 37.2 - - + +
139F THR* 6.3 0.2 - - + -
884F ASP* 3.2 8.6 - - - +
885F PRO* 1.3 94.2 - - + +
887F LEU* 1.3 61.8 + - - +
889F GLN* 3.5 6.9 + - - +
890F GLY* 3.2 18.4 + - - -
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Residues in contact with LEU 887 (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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113F GLU* 6.0 1.8 - - - +
647F ARG* 4.3 10.5 - - - +
651F PRO* 5.9 2.7 - - + -
831F MET* 4.2 16.2 - - + -
881F LEU* 3.8 32.1 - - + -
884F ASP* 3.1 30.7 + - - +
886F PHE* 1.3 73.4 - - - +
888F LYS* 1.3 67.6 + - - +
890F GLY* 3.2 2.4 + - - +
891F LEU* 3.0 40.0 + - + +
1004F FLC 3.8 38.4 - - + +
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Residues in contact with LYS 888 (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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25F PRO* 6.5 1.1 - - + -
834F ALA* 4.9 8.6 - - + +
879F ASP* 5.4 6.3 - - - -
880F ILE* 2.8 47.6 + - - +
881F LEU* 4.0 20.0 - - + +
882F GLU* 5.8 0.7 - - - -
884F ASP 3.1 15.5 + - - +
885F PRO* 3.7 8.7 - - + +
886F PHE 3.3 0.2 - - - -
887F LEU* 1.3 78.6 - - - +
889F GLN* 1.3 62.5 + - - +
891F LEU* 3.4 2.7 + - - +
892F VAL* 3.0 43.7 + - + +
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Residues in contact with GLN 889 (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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24F VAL* 3.5 30.0 - - + +
26F GLY 4.5 0.2 - - - +
28F VAL* 3.4 27.4 + - + +
32F ASP* 2.9 34.0 + - - +
34F LEU* 3.7 21.6 - - - +
35F ILE* 4.0 8.1 - - - +
120F ARG* 4.8 7.1 - - - +
885F PRO 2.9 18.0 + - - +
886F PHE* 3.9 5.4 + - - +
888F LYS* 1.3 77.1 - - - +
890F GLY* 1.3 61.9 + - - +
892F VAL* 3.4 4.9 + - - +
893F LEU* 3.3 35.0 + - + +
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Residues in contact with GLY 890 (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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34F LEU* 4.8 10.8 - - - -
113F GLU* 3.8 27.4 - - - +
886F PHE 3.2 14.7 + - - -
887F LEU* 3.7 3.6 - - - -
889F GLN* 1.3 79.9 - - - +
891F LEU* 1.3 62.8 + - - +
893F LEU* 3.7 6.6 + - - +
894F ARG* 3.5 20.5 + - - +
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Residues in contact with LEU 891 (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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831F MET* 4.4 5.6 - - + +
834F ALA* 4.1 25.6 - - + +
835F LYS* 3.9 32.3 - - + -
881F LEU* 4.2 2.9 - - + -
887F LEU* 3.0 37.4 + - + +
888F LYS* 4.0 3.1 - - - +
890F GLY* 1.3 74.2 - - - +
892F VAL* 1.3 68.6 + - + +
894F ARG* 3.0 52.1 + - - +
895F ASN* 3.6 12.7 + - - +
1004F FLC 3.8 18.6 - - + -
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Residues in contact with VAL 892 (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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23F LEU* 3.5 48.3 - - + +
24F VAL* 4.8 2.2 - - + +
72F GLU* 4.9 15.0 - - + +
888F LYS* 3.0 39.5 + - + +
889F GLN* 3.9 5.6 - - - +
890F GLY 3.4 0.4 - - - -
891F LEU* 1.3 77.3 - - + +
893F LEU* 1.3 64.7 + - + +
894F ARG 3.1 1.9 + - - -
895F ASN* 3.2 21.6 + - - +
896F PRO* 3.5 9.2 - - - +
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Residues in contact with LEU 893 (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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20F LEU* 3.6 44.7 - - + +
23F LEU* 5.1 2.7 - - + -
24F VAL* 5.2 4.7 - - + -
34F LEU* 3.7 37.7 - - + -
35F ILE* 4.3 16.2 - - + -
38F ASP* 3.9 17.9 - - - +
109F ALA* 4.7 2.8 - - + +
889F GLN* 3.3 24.1 + - + +
890F GLY 4.2 4.7 - - - +
891F LEU 3.2 1.0 - - - -
892F VAL* 1.3 84.0 - - + +
894F ARG* 1.3 59.1 + - + +
896F PRO* 4.0 6.8 - - - +
897F TYR* 3.4 21.8 - - - -
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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
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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