Contacts of the helix formed by residues 876 - 890 (chain D) in PDB entry 2O5J
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 SER 876 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792D ILE 4.4 0.5 + - - -
793D THR 4.3 3.1 + - - -
795D VAL* 4.1 10.8 - - - -
860D LEU 3.3 10.2 + - - -
861D GLN 4.4 2.2 - - - -
862D ASP 3.0 24.0 - - - -
863D VAL* 4.7 2.8 - - - +
864D VAL 4.4 3.1 - - - +
875D THR* 1.3 80.5 - - - +
877D PRO* 1.4 67.7 - - - +
878D GLY* 3.9 0.3 - - - -
879D ARG* 2.9 40.9 + - - +
880D ILE* 3.1 19.2 + - - +
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Residues in contact with PRO 877 (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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843D PHE* 5.3 3.4 - - + -
849D ALA* 4.7 13.0 - - + +
850D LEU* 5.0 5.1 - - + +
853D VAL* 3.8 17.7 - - + -
858D VAL* 4.4 4.3 - - + -
859D ASP 3.8 13.0 - - - +
860D LEU* 3.2 33.5 - - + +
862D ASP 3.1 15.5 - - - +
864D VAL* 4.3 15.9 - - + -
866D VAL* 6.1 0.9 - - + -
876D SER* 1.4 80.2 - - - +
878D GLY* 1.3 57.5 + - - +
880D ILE* 3.2 9.5 + - + +
881D LEU* 2.9 29.6 + - - +
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Residues in contact with GLY 878 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792D ILE* 2.9 48.0 - - - +
793D THR* 4.3 0.6 - - - +
860D LEU* 3.0 20.0 + - - +
877D PRO* 1.3 77.4 - - - +
879D ARG* 1.3 55.8 + - - +
881D LEU* 3.3 0.8 + - - -
882D PHE* 3.0 26.5 + - - +
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Residues in contact with ARG 879 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793D THR* 2.9 36.1 - - - +
795D VAL* 3.2 30.1 - - - +
863D VAL* 5.9 0.4 - - - +
874D GLU 5.7 1.0 + - - -
875D THR* 3.4 33.5 + - + +
876D SER* 2.9 16.7 + - - +
878D GLY* 1.3 75.7 - - - +
880D ILE* 1.3 62.0 + - - +
882D PHE* 3.7 10.6 + - - +
883D ALA* 3.4 18.9 + - - +
902D LEU* 2.6 42.4 + - + +
903D ASP* 3.2 21.1 + - - +
904D VAL* 3.9 8.3 + - - +
906D GLN* 4.0 7.2 - - - -
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Residues in contact with ILE 880 (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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846D PRO* 4.9 20.9 - - + +
849D ALA* 5.3 2.5 - - + -
850D LEU* 5.0 8.7 - - + -
866D VAL* 4.5 21.3 - - + -
868D TYR* 4.1 34.6 + - + -
873D LEU* 5.5 5.2 - - + -
875D THR* 3.7 28.3 - - + +
876D SER 3.1 17.3 - - - +
877D PRO* 3.2 10.2 + - + +
879D ARG* 1.3 74.4 - - - +
881D LEU* 1.3 65.2 + - - +
883D ALA* 3.2 17.8 - - - +
884D ARG* 3.3 8.3 + - - +
902D LEU* 4.8 9.6 - - + -
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Residues in contact with LEU 881 (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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792D ILE* 3.9 10.5 - - + -
850D LEU* 3.8 31.1 - - + +
860D LEU* 4.6 16.4 - - + -
877D PRO 2.9 15.9 + - - +
878D GLY* 3.3 5.8 + - - +
880D ILE* 1.3 74.7 - - - +
882D PHE* 1.3 66.3 + - - +
884D ARG* 2.9 43.3 + - - +
885D ILE* 3.0 22.4 + - + +
937D TYR* 5.7 3.1 - - + -
941D PHE* 3.8 28.7 - - + -
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Residues in contact with PHE 882 (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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789D LEU* 6.1 4.5 - - + -
792D ILE* 4.2 3.1 - - + +
793D THR* 4.2 10.8 - - + -
878D GLY 3.0 16.9 + - - +
879D ARG* 3.8 9.9 - - - +
881D LEU* 1.3 75.3 - - - +
883D ALA* 1.3 65.3 + - - +
884D ARG 3.2 0.2 + - - -
885D ILE* 3.3 17.0 + - + +
886D VAL* 3.2 44.7 + - + +
900D ILE* 4.2 25.6 - - + -
901D GLN 4.4 7.6 - - - -
902D LEU* 5.3 3.6 - - + -
906D GLN* 4.0 41.5 - - + -
910D SER* 5.7 1.6 - - - -
911D LEU* 5.8 4.9 - - + -
914D LEU* 4.2 17.9 - - + -
934D LEU* 4.3 22.0 - - + -
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Residues in contact with ALA 883 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868D TYR* 3.9 20.8 + - + +
879D ARG 3.4 10.9 + - - +
880D ILE* 3.2 15.5 - - - +
882D PHE* 1.3 79.7 - - - +
884D ARG* 1.3 52.6 + - - +
886D VAL* 3.9 2.4 - - - +
887D ALA* 2.8 35.2 + - - +
896D ALA* 4.9 1.2 - - - +
897D TRP* 6.4 0.2 - - + -
900D ILE* 4.0 27.2 - - + +
902D LEU* 5.4 8.1 - - + -
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Residues in contact with ARG 884 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ARG* 4.2 38.5 - - - +
847D ASP* 6.0 1.0 - - - +
850D LEU* 3.5 30.7 - - - +
868D TYR* 4.9 2.9 + - - +
880D ILE 3.3 6.8 + - - +
881D LEU* 2.9 30.6 + - - +
883D ALA* 1.3 77.7 - - - +
885D ILE* 1.3 58.0 + - - +
887D ALA* 2.9 7.3 + - + +
888D GLU* 2.5 60.0 + - + +
937D TYR* 5.5 9.4 + - - -
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Residues in contact with ILE 885 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789D LEU* 5.3 3.6 - - + -
792D ILE* 4.8 2.0 - - + -
881D LEU* 3.0 16.9 + - + +
882D PHE* 3.4 30.5 - - + +
884D ARG* 1.3 75.1 - - - +
886D VAL* 1.3 55.3 + - + +
888D GLU* 3.3 6.6 + - - +
889D ALA* 2.8 35.0 + - - +
933D ALA* 4.3 8.8 - - + +
934D LEU* 4.3 19.3 - - + -
937D TYR* 3.6 49.8 - - + -
941D PHE* 4.0 27.6 - - + -
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Residues in contact with VAL 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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882D PHE* 3.2 47.7 + - + +
883D ALA* 3.9 4.3 - - - +
885D ILE* 1.3 73.3 - - + +
887D ALA* 1.3 66.9 + - - +
888D GLU 3.1 1.0 + - - -
889D ALA* 3.3 0.9 + - - +
890D VAL* 3.1 35.2 + - + +
896D ALA* 4.1 12.6 - - + +
899D LEU* 4.6 5.2 - - + -
900D ILE* 4.1 21.1 - - + -
914D LEU* 4.2 11.7 - - + -
930D LEU* 4.0 26.7 - - + -
934D LEU* 4.7 2.2 - - + -
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Residues in contact with ALA 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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868D TYR* 5.3 2.0 - - - +
883D ALA 2.8 23.0 + - - +
884D ARG* 2.9 10.5 + - + +
886D VAL* 1.3 75.5 - - - +
888D GLU* 1.3 58.6 + - + +
890D VAL 2.8 19.1 - - - +
891D GLU* 3.7 9.9 - - - +
893D GLU* 4.0 31.3 - - + +
896D ALA* 3.7 15.9 - - + +
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Residues in contact with GLU 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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176B ARG* 4.0 16.8 + - - -
198B ARG* 5.4 5.4 + - - -
200B TRP* 5.4 10.1 - - - -
884D ARG* 2.5 48.0 + - + +
885D ILE* 3.5 6.5 - - - +
887D ALA* 1.3 75.1 - - + +
889D ALA* 1.3 67.1 - - - +
890D VAL 2.9 3.4 + - - -
891D GLU* 3.6 10.8 + - - +
937D TYR* 5.7 4.9 - - - +
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Residues in contact with ALA 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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885D ILE 2.8 20.2 + - - +
886D VAL 3.6 5.2 - - - +
888D GLU* 1.3 72.2 - - - +
890D VAL* 1.3 63.5 + - - +
891D GLU 4.3 0.5 + - - -
926D LYS* 5.3 1.0 - - - -
929D ARG* 4.0 19.2 - - - +
930D LEU* 3.6 34.3 - - + +
933D ALA* 3.7 18.4 - - + -
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Residues in contact with VAL 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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886D VAL* 3.1 25.1 - - + +
887D ALA* 2.8 20.2 - - - +
888D GLU 3.0 0.2 - - - -
889D ALA* 1.3 82.4 - - + +
891D GLU* 1.3 50.9 + - - +
892D ASP* 2.9 23.0 + - + +
896D ALA* 4.7 8.7 - - + +
899D LEU* 6.1 1.3 - - + -
922D LEU* 3.3 38.6 - - + -
926D LYS* 3.6 38.6 - - - +
930D LEU* 4.7 6.1 - - + -
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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