Contacts of the helix formed by residues 848 - 861 (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 TRP 848 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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840D TRP* 3.2 62.5 + + + +
841D ARG 4.7 1.4 + - - +
842D ASN* 4.6 20.4 - - + +
846D GLY 4.6 2.0 - - - -
847D SER* 1.3 72.8 - - - +
849D PHE* 1.3 59.2 + - - +
851D GLN* 3.4 8.5 - - - +
852D SER* 2.5 34.7 + - - -
877D VAL* 4.3 9.0 - - + -
880D PHE* 3.3 57.5 - + + -
881D GLU* 3.6 45.8 - - - -
883D LYS 3.9 3.8 - - - -
885D GLN* 3.8 29.6 - - + +
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Residues in contact with PHE 849 (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* 3.8 17.3 - - + -
782C ILE 4.3 2.7 - - - -
783C GLN* 3.3 16.6 - - + +
830D ALA* 3.7 27.1 - - + -
831D TYR 3.7 14.8 - - - -
832D SER* 3.2 38.8 - - - +
840D TRP 4.8 0.2 + - - -
847D SER* 3.3 0.8 + - - -
848D TRP* 1.3 80.1 - - - +
850D ILE* 1.3 66.3 - - + +
852D SER* 3.4 1.6 + - - -
853D LEU* 2.8 43.8 + - + +
870D LEU* 5.4 4.7 - - + -
873D VAL* 3.7 25.8 - - + -
874D ASN* 5.3 0.2 - - - -
877D VAL* 4.0 7.6 - - + +
885D GLN* 4.2 5.6 - - - +
887D PRO* 4.0 17.3 - - + -
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Residues in contact with ILE 850 (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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685C ASP* 3.4 36.1 - - + +
688C ASN* 5.0 1.3 - - - +
689C LEU* 3.9 33.2 - - + -
733C VAL* 4.8 0.2 - - + -
735C LEU* 4.1 11.0 - - + -
781C ILE* 4.3 16.4 - - + -
783C GLN* 3.9 15.0 - - + +
847D SER* 3.2 21.4 + - - +
849D PHE* 1.3 89.6 - - + +
851D GLN* 1.3 66.0 + - - +
853D LEU* 3.8 7.4 - - + +
854D CYS* 3.1 27.0 + - - -
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Residues in contact with GLN 851 (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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685C ASP* 4.4 1.7 + - - +
688C ASN* 4.1 14.8 + - - +
842D ASN* 4.6 2.1 - - - +
845D ASP* 3.0 35.9 - - - +
846D GLY 3.0 24.9 - - - +
847D SER 3.2 12.6 + - - +
848D TRP* 3.4 11.2 - - - +
850D ILE* 1.3 77.3 - - - +
852D SER* 1.3 59.8 + - - +
854D CYS* 4.1 1.6 - - - +
855D ALA* 3.2 26.5 + - - +
876D LYS* 5.6 0.7 - - - -
880D PHE* 3.8 26.7 - - + -
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Residues in contact with SER 852 (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 2.5 23.6 + - - -
849D PHE 3.6 3.8 - - - -
851D GLN* 1.3 76.7 - - - +
853D LEU* 1.3 65.8 + - - +
855D ALA* 3.2 1.4 + - - +
856D MET* 3.0 29.3 + - - +
873D VAL* 4.2 7.6 - - - -
876D LYS* 3.8 25.0 - - - +
877D VAL* 3.6 16.2 - - - +
880D PHE* 3.6 22.7 - - - -
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Residues in contact with LEU 853 (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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689C LEU* 4.9 9.2 - - + -
781C ILE* 3.6 46.0 - - + -
830D ALA* 5.8 0.4 - - + -
849D PHE* 2.8 29.9 + - + +
850D ILE* 3.8 12.3 - - + +
852D SER* 1.3 76.5 - - - +
854D CYS* 1.3 62.4 + - - +
856D MET* 4.0 1.0 - - - +
857D LEU* 3.2 42.5 + - + +
866D PHE* 5.2 3.4 - - + -
869D ILE* 5.4 1.3 - - + -
870D LEU* 4.0 26.0 - - + -
873D VAL* 3.7 18.3 - - + +
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Residues in contact with CYS 854 (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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688C ASN* 3.1 35.0 - - - +
689C LEU* 3.7 39.7 - - - -
692C THR* 3.5 24.3 + - - +
850D ILE* 3.1 16.6 + - - +
851D GLN 4.1 0.2 - - - +
853D LEU* 1.3 77.4 - - - +
855D ALA* 1.3 62.4 + - - +
857D LEU* 3.5 6.0 + - - +
858D LYS* 2.9 34.4 + - - +
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Residues in contact with ALA 855 (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 3.2 19.0 + - - +
852D SER* 3.2 6.7 + - - +
854D CYS* 1.3 77.6 - - - +
856D MET* 1.3 74.3 + - + +
858D LYS* 3.2 21.4 + - - +
859D GLN* 3.2 24.7 + - - +
876D LYS* 4.5 9.9 - - - +
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Residues in contact with MET 856 (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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852D SER 3.0 18.0 + - - +
853D LEU 4.0 0.4 - - - +
855D ALA* 1.3 79.5 - - + +
857D LEU* 1.3 62.3 + - - +
859D GLN* 3.2 18.4 + - - +
860D TYR* 2.8 53.3 + - + +
869D ILE* 4.1 12.1 - - + +
872D ARG* 3.7 23.3 - - + +
873D VAL* 3.6 35.9 - - + +
876D LYS* 3.8 27.8 - - + +
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Residues in contact with LEU 857 (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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692C THR* 3.9 25.6 - - + -
693C PHE* 4.1 24.7 - - + -
696C LEU* 4.6 6.1 - - + -
853D LEU* 3.2 40.3 + - + +
854D CYS* 3.8 5.4 - - - +
855D ALA 3.3 0.2 - - - -
856D MET* 1.3 75.8 - - - +
858D LYS* 1.3 62.8 - - - +
861D ALA* 3.0 39.0 + - + +
866D PHE* 4.3 7.4 - - + -
869D ILE* 4.3 17.7 - - + -
900D PHE* 3.9 31.6 - - + -
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Residues in contact with LYS 858 (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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688C ASN* 3.0 26.2 + - - +
691C GLU* 6.2 2.2 - - - +
692C THR* 3.5 29.6 - - + +
854D CYS* 2.9 22.9 + - - +
855D ALA* 3.2 12.6 + - - +
857D LEU* 1.3 77.4 - - - +
859D GLN* 1.3 62.4 + - + +
862D ASP* 4.9 3.8 - - - +
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Residues in contact with GLN 859 (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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855D ALA* 3.2 20.0 - - - +
856D MET* 3.2 16.5 + - - +
857D LEU 3.1 0.4 - - - -
858D LYS* 1.3 84.8 - - + +
860D TYR* 1.3 95.2 + - + +
861D ALA 3.8 0.7 - - - -
862D ASP* 3.7 1.8 - - - +
863D LYS* 3.2 26.3 + - - -
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Residues in contact with TYR 860 (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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856D MET* 2.8 50.8 + - + +
859D GLN* 1.3 102.7 + - + +
861D ALA* 1.3 60.2 + - - +
862D ASP 3.1 3.1 - - - -
863D LYS* 3.8 17.0 - - + +
864D LEU* 3.0 54.9 + - + -
869D ILE* 3.1 17.0 - - + +
872D ARG* 3.5 37.4 + - + -
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Residues in contact with ALA 861 (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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696C LEU* 3.8 29.2 - - + -
857D LEU* 3.0 32.2 + - + +
859D GLN 3.8 1.2 - - - -
860D TYR* 1.3 76.1 - - - +
862D ASP* 1.3 58.2 + - + +
863D LYS 3.4 0.2 - - - -
864D LEU 4.5 2.4 - - - +
869D ILE* 3.8 11.5 - - - +
900D PHE* 3.9 18.9 + - + +
901D TYR* 3.4 18.7 - - - -
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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
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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