Contacts of the helix formed by residues 884 - 893 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135D GLY 4.4 7.6 - - - +
136D SER* 3.9 29.1 - - - +
651D PRO* 6.1 0.2 - - - +
827D ASP* 6.0 2.3 - - - -
881D LEU* 3.2 24.7 + - + +
883D GLY* 1.3 92.4 - - - +
885D PRO* 1.3 68.5 - - - +
886D PHE* 3.2 4.1 + - + -
887D LEU* 3.3 21.7 + - + +
888D LYS* 3.1 17.3 + - - +
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Residues in contact with PRO 885 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D VAL* 3.7 22.4 - - + +
881D LEU 4.0 2.4 - - - +
882D GLU 4.3 9.9 - - - +
883D GLY 3.6 8.3 - - - +
884D ASP* 1.3 88.2 - - - +
886D PHE* 1.3 67.8 + - + +
888D LYS* 3.6 10.2 - - + +
889D GLN* 2.9 31.5 + - - +
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Residues in contact with PHE 886 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D VAL* 3.5 50.9 - - + -
29D SER* 4.3 10.1 - - - -
120D ARG* 3.7 40.9 + - - +
126D LEU* 4.1 22.9 - - + -
136D SER* 5.1 6.1 - - - +
138D THR* 3.5 36.3 - - + -
884D ASP* 3.2 1.7 - - + -
885D PRO* 1.3 88.3 - - + +
887D LEU* 1.3 58.2 + - - +
889D GLN* 3.3 6.6 + - - +
890D GLY* 3.0 24.3 + - - -
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Residues in contact with LEU 887 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D GLU* 5.9 3.6 - - - +
136D SER* 5.6 3.5 + - - +
647D ARG* 4.4 10.8 - - - +
651D PRO* 6.2 1.1 - - + -
679D PHE* 6.4 1.1 - - + -
831D MET* 4.2 16.4 - - + -
881D LEU* 3.6 32.8 - - + -
884D ASP* 3.3 21.9 + - + +
886D PHE* 1.3 76.4 - - - +
888D LYS* 1.3 67.3 + - - +
890D GLY* 3.1 3.0 + - - +
891D LEU* 3.0 39.0 + - + +
1001D PG0 3.9 37.5 - - - +
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Residues in contact with LYS 888 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D PRO* 6.5 1.3 - - - -
834D ALA* 5.8 2.0 - - + -
879D ASP* 4.3 10.5 - - - +
880D ILE* 2.7 50.2 + - + +
881D LEU* 4.0 23.9 - - + +
882D GLU* 5.8 0.9 - - - -
884D ASP 3.1 14.6 + - - +
885D PRO* 3.6 11.4 - - + +
887D LEU* 1.3 75.2 - - - +
889D GLN* 1.3 57.8 + - - +
891D LEU* 3.4 3.4 + - - +
892D VAL* 2.9 49.1 + - + +
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Residues in contact with GLN 889 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D VAL* 3.9 21.2 - - + +
26D GLY 3.7 16.2 + - - -
28D VAL* 3.9 18.9 - - + +
32D ASP* 3.0 36.7 + - - +
34D LEU* 3.8 16.7 - - + +
35D ILE* 5.1 3.6 - - - +
120D ARG* 5.3 4.9 + - - -
885D PRO 2.9 17.3 + - - +
886D PHE* 3.8 6.4 - - - +
888D LYS* 1.3 73.5 - - - +
890D GLY* 1.3 64.8 + - - +
892D VAL* 3.2 19.4 - - - +
893D LEU* 3.2 25.1 - - + +
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Residues in contact with GLY 890 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 4.6 10.4 - - - +
113D GLU* 3.7 27.5 - - - +
886D PHE 3.0 15.3 + - - -
887D LEU* 3.1 4.0 + - - -
889D GLN* 1.3 77.6 - - - +
891D LEU* 1.3 65.9 + - - +
893D LEU* 3.9 5.7 + - - +
894D ARG* 3.4 21.0 + - - +
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Residues in contact with LEU 891 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D GLU* 5.6 0.4 - - - +
831D MET* 4.5 6.7 - - + +
834D ALA* 4.3 23.3 - - + +
835D LYS* 3.7 35.4 - - + -
881D LEU* 4.3 4.3 - - + -
887D LEU* 3.0 32.8 + - + +
888D LYS* 3.9 3.4 - - - +
890D GLY* 1.3 74.5 - - - +
892D VAL* 1.3 66.6 + - + +
893D LEU 3.1 3.3 + - - -
894D ARG* 3.2 37.7 + - - +
895D ASN* 3.6 16.2 + - - +
1001D PG0 3.9 23.8 - - - +
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Residues in contact with VAL 892 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 3.8 22.7 - - + +
24D VAL* 3.3 31.2 - - + -
72D GLU* 5.0 9.2 - - + +
888D LYS* 2.9 44.6 + - + +
889D GLN* 3.2 16.6 - - - +
891D LEU* 1.3 77.1 - - + +
893D LEU* 1.3 65.2 + - + +
895D ASN* 3.5 22.7 + - - +
896D PRO* 3.6 9.0 - - - +
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Residues in contact with LEU 893 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D LEU* 3.8 28.6 - - + +
23D LEU* 4.4 5.6 - - + -
24D VAL* 3.8 13.7 - - + -
34D LEU* 3.9 24.5 - - + -
35D ILE* 3.8 31.0 - - + +
38D ASP* 3.9 18.9 - - - +
109D ALA* 5.0 2.5 - - + +
889D GLN* 3.2 35.3 + - + +
890D GLY 3.9 3.1 + - - +
891D LEU 3.1 0.8 - - - -
892D VAL* 1.3 79.6 - - + +
894D ARG* 1.3 62.6 + - - +
896D PRO* 3.7 8.6 - - - +
897D TYR* 3.4 20.3 - - - -
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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
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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