Contacts of the helix formed by residues 865 - 879 (chain D) in PDB entry 1RHM
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 GLU 865 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B HIS* 2.9 34.1 + - + +
864D LEU* 1.3 76.5 - - - +
866D PHE* 1.3 77.3 + - - +
867D MET* 2.9 36.3 + - - +
868D HIS* 3.1 20.7 + - - +
869D ILE* 3.2 8.4 + - - +
894D LEU* 5.4 1.7 - - - +
896D LYS 4.7 1.0 - - - +
897D GLU* 3.7 9.7 - - + -
898D LEU* 2.8 39.5 + - - +
899D TYR* 3.6 35.2 - - + +
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Residues in contact with PHE 866 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693C PHE* 6.4 1.1 - + - -
779C LEU* 3.8 20.2 - - + -
781C ILE* 5.4 12.6 - - + -
828D LEU* 3.1 37.0 - - + -
830D ALA* 5.8 1.3 - - + -
853D LEU* 5.2 2.9 - - + -
857D LEU* 4.3 14.1 - - + -
864D LEU 3.7 0.8 + - - -
865D GLU* 1.3 74.0 - - - +
867D MET* 1.3 66.3 + - + +
869D ILE* 3.1 13.9 + - + -
870D LEU* 3.1 45.6 + - + +
894D LEU* 5.1 0.4 - - + -
898D LEU* 2.7 46.3 + - + +
900D PHE* 3.5 28.9 - + + -
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Residues in contact with MET 867 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B MET* 4.4 31.4 - - + +
368B HIS* 4.9 0.9 - - + -
371B THR* 5.0 10.5 - - - +
389B ILE* 6.3 1.8 - - - -
828D LEU* 3.5 35.0 - - + -
865D GLU* 2.9 26.5 + - - +
866D PHE* 1.3 77.4 - - + +
868D HIS* 1.3 61.5 + - + +
870D LEU* 3.5 10.3 + - + +
871D THR* 3.0 26.0 + - - -
889D ILE* 3.9 31.1 - - + +
892D SER* 4.0 19.3 - - - +
894D LEU* 4.5 9.2 - - + -
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Residues in contact with HIS 868 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B GLU* 3.0 45.4 + - + +
367B MET* 4.8 2.7 - - + -
368B HIS* 3.5 35.8 + + - -
397B GLU* 3.8 35.6 + - + +
399B TYR* 4.4 2.2 - - - -
864D LEU* 4.4 16.5 - - + +
865D GLU* 3.1 14.9 + - - +
867D MET* 1.3 81.8 - - + +
869D ILE* 1.3 67.0 + - - +
871D THR* 3.3 9.0 + - - -
872D ARG* 3.2 27.1 + - - +
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Residues in contact with ILE 869 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853D LEU* 5.4 0.2 - - + -
856D MET* 4.1 22.9 - - + +
857D LEU* 4.3 24.0 - - + +
860D TYR* 3.1 36.1 - - + +
861D ALA* 3.8 9.4 - - - +
864D LEU* 3.4 26.0 - - + +
865D GLU 3.2 12.5 + - - +
866D PHE* 3.1 19.0 + - + +
868D HIS* 1.3 78.3 - - - +
870D LEU* 1.3 58.2 + - + +
872D ARG* 3.1 11.7 + - - +
873D VAL* 3.0 29.2 + - + +
900D PHE* 5.1 3.4 - - + -
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Residues in contact with LEU 870 (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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781C ILE* 6.5 0.2 - - + -
828D LEU* 4.0 2.5 - - + -
830D ALA* 4.0 27.8 - - + -
849D PHE* 5.4 3.8 - - + -
853D LEU* 4.0 27.6 - - + -
866D PHE* 3.1 40.1 + - + +
867D MET* 3.9 14.8 - - + +
868D HIS 3.3 0.2 - - - -
869D ILE* 1.3 75.1 - - + +
871D THR* 1.3 57.7 + - - +
872D ARG 3.3 0.2 - - - -
873D VAL* 3.5 11.1 - - + +
874D ASN* 3.0 33.3 + - - +
889D ILE* 3.4 40.8 - - + +
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Residues in contact with THR 871 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B MET* 5.0 9.9 - - - +
392B SER* 5.1 3.5 + - - -
394B LEU* 4.2 7.8 + - + +
395B THR 3.5 28.2 - - - +
396B LYS* 3.8 19.5 - - - +
397B GLU* 4.4 7.4 - - + +
867D MET 3.0 14.8 + - - -
868D HIS* 3.5 15.1 - - - +
869D ILE 3.1 0.2 - - - -
870D LEU* 1.3 74.9 - - - +
872D ARG* 1.3 62.2 + - + +
874D ASN* 3.3 8.3 + - - +
875D ARG* 3.0 24.0 + - - +
889D ILE* 4.3 8.7 - - - +
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Residues in contact with ARG 872 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ASN* 3.2 38.8 - - - +
397B GLU* 4.8 8.5 + - - -
856D MET* 3.7 22.7 - - + +
860D TYR* 3.5 35.5 + - + -
864D LEU* 3.8 27.5 - - + +
868D HIS 3.2 17.1 + - - +
869D ILE* 3.1 10.3 + - - +
871D THR* 1.3 75.3 - - + +
873D VAL* 1.3 64.4 + - - +
875D ARG* 3.2 32.2 + - - +
876D LYS* 3.0 24.6 + - - +
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Residues in contact with VAL 873 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849D PHE* 3.7 35.9 - - + -
852D SER* 4.1 6.5 - - - +
853D LEU* 3.7 39.7 - - + +
856D MET* 3.6 23.1 - - + -
869D ILE* 3.0 20.7 + - + +
870D LEU* 3.5 13.9 - - + +
872D ARG* 1.3 77.3 - - - +
874D ASN* 1.3 65.1 + - - +
876D LYS* 3.6 3.7 - - - +
877D VAL* 3.1 24.7 + - + +
887D PRO* 4.8 0.4 - - + -
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Residues in contact with ASN 874 (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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392B SER 4.0 4.8 + - - -
393B MET* 3.6 17.0 - - - +
394B LEU 3.5 22.2 + - - +
395B THR* 5.1 0.4 - - - -
849D PHE* 5.3 0.5 - - - -
870D LEU 3.0 20.6 + - - +
871D THR* 3.3 11.0 - - - +
872D ARG 3.1 0.2 - - - -
873D VAL* 1.3 79.7 - - - +
875D ARG* 1.3 61.9 + - - +
878D ALA* 3.2 25.0 + - - +
886D ILE* 3.8 7.8 - - + +
887D PRO* 3.1 52.9 + - - +
889D ILE* 3.9 14.6 - - - +
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Residues in contact with ARG 875 (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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150A ASP 4.3 6.8 + - - -
151A ASN* 3.6 34.1 + - - +
395B THR* 2.9 60.7 + - + +
396B LYS* 4.2 21.9 - - - +
871D THR* 3.0 13.1 + - - +
872D ARG* 3.2 34.3 + - - +
874D ASN* 1.3 75.4 - - - +
876D LYS* 1.3 58.8 + - - +
878D ALA* 3.3 1.9 + - - +
879D THR* 2.9 46.7 + - + +
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Residues in contact with LYS 876 (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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851D GLN* 5.3 0.4 - - - -
852D SER* 3.8 31.4 - - - +
855D ALA* 4.5 9.1 - - - +
856D MET* 3.8 29.8 - - + +
872D ARG 3.0 15.8 + - - +
873D VAL* 3.6 6.1 - - - +
875D ARG* 1.3 77.6 - - - +
877D VAL* 1.3 56.8 + - - +
879D GLU* 2.9 72.3 + - + +
880D PHE* 3.6 12.3 - - + -
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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
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848D TRP* 4.1 11.1 - - + +
849D PHE* 4.0 16.4 - - - +
852D SER* 3.6 23.3 - - - +
873D VAL* 3.1 18.3 + - + +
876D LYS* 1.3 75.5 - - - +
878D ALA* 1.3 60.7 + - - +
880D PHE* 3.5 29.7 + - - +
885D GLN* 3.4 39.4 + - + +
887D PRO* 3.7 27.8 - - + -
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Residues in contact with ALA 878 (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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320B LYS 3.7 4.2 - - - +
321B ILE* 4.1 5.1 - - + -
322B PRO* 3.6 30.8 - - + +
325B ALA* 5.0 3.6 - - + -
395B THR* 5.0 5.8 - - + +
874D ASN 3.2 15.9 + - - +
875D ARG* 3.9 4.5 - - - +
877D VAL* 1.3 81.2 - - - +
879D THR* 1.3 60.1 + - - +
884D LYS* 2.9 20.7 + - - -
885D GLN 3.5 12.8 - - - +
886D ILE* 4.0 11.9 - - + -
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Residues in contact with THR 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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320B LYS 4.7 4.3 - - - +
321B ILE* 5.1 7.9 - - - +
395B THR* 5.2 2.3 - - - +
875D ARG* 2.9 32.1 + - + +
876D LYS* 4.7 0.4 - - - -
878D ALA* 1.3 80.8 - - - +
879D GLU* 1.3 75.4 + - + +
880D PHE 3.5 1.1 - - - -
884D LYS* 3.5 12.0 + - - +
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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