Contacts of the helix formed by residues 875 - 891 (chain D) in PDB entry 1SOJ
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 875 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781D HIS* 3.4 39.5 + - + +
874D LEU* 1.3 75.0 - - - +
876D HIS* 1.3 65.9 + - - +
877D VAL* 3.4 11.3 + - - +
878D GLU* 2.7 52.8 + - - +
879D PHE* 2.9 20.3 + - - +
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Residues in contact with HIS 876 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875D ASP* 1.3 73.5 - - - +
877D VAL* 1.3 66.4 + - + +
879D PHE* 3.8 5.8 - - - +
880D LYS* 3.0 30.8 + - + +
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Residues in contact with VAL 877 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981A SER* 3.3 30.3 - - - +
875D ASP* 3.1 10.8 + - - +
876D HIS* 1.3 81.2 - - + +
878D GLU* 1.3 67.4 + - + +
880D LYS* 3.5 6.2 - - - +
881D ARG* 3.0 26.3 + - + +
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Residues in contact with GLU 878 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713D PHE* 5.4 5.6 - - - -
779D ILE* 5.2 0.7 - - - +
781D HIS* 2.7 42.4 + - - +
809D LEU* 3.9 24.3 - - + +
874D LEU* 3.3 22.3 - - + +
875D ASP* 2.7 43.8 + - - +
877D VAL* 1.3 75.4 - - + +
879D PHE* 1.3 56.4 + - - +
881D ARG* 3.4 4.0 + - - +
882D PHE* 2.9 28.8 + - - +
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Residues in contact with PHE 879 (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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837C ASN* 5.0 11.9 - - - -
859D TRP* 3.8 26.7 - + - -
862D TYR* 4.1 17.5 - + - -
863D LEU* 4.6 11.0 - - + -
869D ASN* 5.2 2.2 - - - -
871D LEU* 3.8 42.6 - - + -
874D LEU* 4.1 12.5 - - + +
875D ASP 2.9 16.2 + - - +
876D HIS* 3.8 6.7 - - - +
878D GLU* 1.3 73.2 - - - +
880D LYS* 1.3 81.3 + - + +
882D PHE* 2.9 8.0 + + - +
883D ARG* 2.8 36.2 + - + +
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Residues in contact with LYS 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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834C VAL* 3.4 36.2 + - - -
835C ALA* 4.0 12.2 + - - +
837C ASN* 3.4 25.9 + - - +
846C ASP* 5.8 0.7 - - - -
876D HIS* 3.0 19.0 + - + +
877D VAL* 3.5 5.8 - - - +
879D PHE* 1.3 90.5 - - + +
881D ARG* 1.3 62.6 + - - +
883D ARG* 3.5 13.3 + - + +
884D PHE* 3.1 22.3 + - - +
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Residues in contact with ARG 881 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981A SER* 5.4 8.3 - - - -
982A PRO 5.9 2.5 - - - -
983A GLN* 4.8 10.9 + - - -
809D LEU* 4.0 16.8 - - + +
810D GLU* 3.0 36.0 + - - +
877D VAL* 3.0 18.8 + - + +
878D GLU* 3.7 5.2 - - - +
880D LYS* 1.3 74.0 - - - +
882D PHE* 1.3 61.8 + - - +
884D PHE* 3.2 15.7 + - + +
885D LEU* 2.9 56.9 + - + +
922D GLU* 4.3 27.0 + - - +
926D LEU* 6.3 0.6 - - - +
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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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809D LEU* 4.0 14.6 - - + +
812D MET* 3.7 24.9 - - + -
813D ALA* 3.3 35.2 - - + -
816D VAL* 3.7 33.2 - - + -
859D TRP* 3.9 18.4 - + - -
871D LEU* 3.4 33.4 - - + -
874D LEU* 4.4 7.4 - - + -
878D GLU 2.9 14.4 + - - +
879D PHE* 2.9 14.0 + + - +
881D ARG* 1.3 76.7 - - - +
883D ARG* 1.3 64.9 + - - +
885D LEU* 3.1 9.3 + - - +
886D VAL* 2.9 32.1 + - + +
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Residues in contact with ARG 883 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834C VAL* 4.9 1.4 + - - +
837C ASN* 3.7 21.2 + - - -
841C ALA* 3.8 3.0 + - - +
842C VAL* 3.4 40.7 + - - +
845C ASN* 3.8 12.7 + - - +
846C ASP* 2.5 45.1 + - - -
859D TRP* 3.5 47.6 - - + +
863D LEU* 5.9 2.9 - - - +
879D PHE* 2.8 28.6 + - + +
880D LYS* 3.7 12.8 - - - +
882D PHE* 1.3 78.9 - - - +
884D PHE* 1.3 61.7 + - - +
886D VAL* 3.3 1.6 + - - +
887D ILE* 3.1 37.5 + - - +
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Residues in contact with PHE 884 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846C ASP* 5.9 1.5 + - - -
847C ARG* 6.2 1.3 - - - -
880D LYS 3.1 12.6 + - - +
881D ARG* 3.5 18.6 - - - +
883D ARG* 1.3 80.2 - - - +
885D LEU* 1.3 78.8 - - + +
887D ILE* 3.6 7.9 + - + +
888D GLU* 3.0 69.8 + - + +
926D LEU* 4.4 10.3 - - + -
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Residues in contact with LEU 885 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809D LEU* 4.8 3.4 - - + -
810D GLU* 3.5 39.0 - - + +
813D ALA* 3.6 16.8 - - + -
881D ARG* 2.9 50.4 + - + +
882D PHE* 3.5 6.1 - - - +
884D PHE* 1.3 98.0 - - + +
886D VAL* 1.3 66.9 + - - +
888D GLU* 3.3 5.0 + - - +
889D ALA* 3.1 22.3 + - - +
926D LEU* 4.5 20.8 - - + +
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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
----------------------------------------------------------
813D ALA* 3.5 28.7 - - - +
816D VAL* 4.5 4.5 - - + -
817D ALA* 4.1 11.7 - - + -
820D MET* 3.9 21.5 - - - -
859D TRP* 3.6 23.8 - - + +
882D PHE* 2.9 38.9 + - + +
883D ARG 3.7 4.3 - - - +
885D LEU* 1.3 74.6 - - - +
887D ILE* 1.3 64.8 + - - +
889D ALA* 3.0 4.7 + - - +
890D ILE* 2.9 31.3 + - + +
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Residues in contact with ILE 887 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845C ASN* 3.5 54.7 - - + +
846C ASP* 4.3 3.4 - - - +
847C ARG* 4.7 5.6 - - - -
855D ALA* 4.5 4.5 - - + -
859D TRP* 4.0 14.6 - - + +
883D ARG* 3.1 39.9 + - + +
884D PHE* 3.9 7.6 - - + +
886D VAL* 1.3 75.7 - - - +
888D GLU* 1.3 66.4 + - - +
890D ILE* 3.4 5.2 + - - +
891D LEU* 2.9 47.6 + - + +
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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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847C ARG* 3.2 30.7 + - - -
884D PHE* 3.0 56.6 + - + +
885D LEU* 3.6 5.4 - - - +
887D ILE* 1.3 77.4 - - - +
889D ALA* 1.3 63.4 + - - +
891D LEU* 3.7 4.4 + - - +
892D ALA 3.4 11.6 + - - -
926D LEU* 4.0 19.1 - - + +
930D GLN* 3.1 34.6 + - - +
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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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813D ALA 5.6 0.2 - - - -
814D LEU* 4.5 13.9 - - + -
817D ALA* 3.6 19.3 - - + -
885D LEU 3.1 11.1 + - - +
886D VAL* 3.0 8.8 + - - +
888D GLU* 1.3 74.4 - - - +
890D ILE* 1.3 68.7 + - - +
892D ALA 2.9 9.2 + - - -
893D THR* 3.7 1.0 + - - +
926D LEU* 5.2 2.0 - - + +
929D CYS* 6.0 1.3 - - + -
930D GLN* 4.5 6.7 - - + +
933D ILE* 2.8 39.7 - - + +
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Residues in contact with ILE 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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817D ALA* 3.8 19.3 - - + +
820D MET* 3.8 37.2 - - + +
821D HIS* 4.1 22.2 - - - +
851D GLU* 3.6 25.9 - - - +
855D ALA* 3.9 27.4 - - + +
886D VAL* 2.9 29.0 + - + +
887D ILE 3.9 2.9 - - - +
889D ALA* 1.3 75.0 - - - +
891D LEU* 1.3 58.5 + - - +
892D ALA 3.0 3.3 + - - -
893D THR* 2.6 33.8 + - - -
933D ILE* 6.3 0.2 - - - -
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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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845C ASN* 4.9 2.2 - - + +
847C ARG* 3.2 46.0 - - - +
848D SER* 4.2 9.5 + - - +
851D GLU* 3.9 10.3 - - + +
852D ASN* 3.6 51.6 - - - +
855D ALA* 5.3 0.9 - - + -
887D ILE* 2.9 36.8 + - + +
888D GLU* 4.3 3.4 - - - +
890D ILE* 1.3 77.3 - - + +
892D ALA* 1.3 58.2 + - - +
893D THR 3.2 2.0 + - - -
894D ASP* 3.7 16.5 + - - +
897D LYS* 5.8 0.9 - - - +
901D PHE* 4.7 4.7 - - - -
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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
------------------------------------------------------------
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