Contacts of the helix formed by residues 876 - 887 (chain D) in PDB entry 3RMD
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 PHE 876 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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741D VAL* 3.7 16.6 - - + -
744D ALA* 3.7 22.9 - - + -
745D LEU* 3.5 23.5 - - + +
748D CYS* 4.0 19.3 - - - -
763D TYR* 5.3 1.1 - + - -
764D PHE* 3.4 37.7 - + - -
767D PHE* 3.9 22.7 - + + -
768D GLU* 5.5 3.8 - - - -
872D LEU* 3.4 30.1 + - + +
875D THR* 1.3 85.0 + - - +
877D ILE* 1.3 77.2 + - + +
879D PRO* 3.1 7.5 - - - +
880D LEU* 3.1 29.8 + - + +
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Residues in contact with ILE 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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764D PHE* 4.3 11.2 - - + -
768D GLU* 4.6 7.4 - - - +
872D LEU* 3.1 31.6 + - + +
873D GLU* 3.6 28.9 - - + +
876D PHE* 1.3 87.1 - - + +
878D LYS* 1.3 71.2 + - - +
880D LEU* 3.1 5.8 + - - +
881D GLU* 3.1 18.9 + - + +
891D TYR* 4.0 27.8 + - + +
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Residues in contact with LYS 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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873D GLU* 2.8 29.4 + - - +
874D LYS* 4.2 10.5 - - + +
877D ILE* 1.3 76.2 - - - +
879D PRO* 1.3 72.8 - - + +
881D GLU* 2.9 27.8 + - - +
882D GLY* 3.5 1.2 + - - -
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Residues in contact with PRO 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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731D GLU* 5.0 20.0 - - + +
745D LEU* 4.2 19.1 - - + -
874D LYS 4.2 5.4 - - - +
875D THR* 3.5 10.1 - - - +
876D PHE* 3.1 37.0 - - - +
878D LYS* 1.3 96.3 - - + +
880D LEU* 1.3 55.6 + - - -
881D GLU 3.5 0.3 + - - -
882D GLY* 3.6 4.4 + - - -
883D PHE* 3.1 38.5 - - + -
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Residues in contact with LEU 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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745D LEU* 4.5 7.0 - - + -
748D CYS* 3.7 41.5 - - + -
752D MET* 4.9 2.7 - - - -
760D LEU* 4.4 4.7 - - + -
764D PHE* 3.8 31.2 - - + -
876D PHE* 3.1 22.2 + - + +
877D ILE 3.6 4.7 - - - +
878D LYS 2.9 1.2 + - - -
879D PRO* 1.3 76.6 - - - +
881D GLU* 1.3 60.3 + - - +
883D PHE* 3.5 16.1 + - + -
884D THR* 3.0 36.6 + - + -
891D TYR* 4.0 15.7 - - + -
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Residues in contact with GLU 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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877D ILE* 3.1 9.2 + - + +
878D LYS* 2.9 23.8 + - - +
880D LEU* 1.3 75.1 - - - +
882D GLY* 1.3 80.3 + - - +
884D THR* 2.8 8.6 + - - -
885D SER* 2.5 49.9 + - - -
891D TYR* 4.0 19.9 - - + +
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Residues in contact with GLY 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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703D THR* 5.2 6.0 - - - +
878D LYS 3.5 4.2 + - - -
879D PRO 3.6 4.6 + - - -
880D LEU 3.3 0.6 - - - -
881D GLU* 1.3 95.1 + - - +
883D PHE* 1.3 66.2 + - - +
885D SER* 3.6 3.1 - - - -
886D ALA* 2.9 25.5 + - - +
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Residues in contact with PHE 883 (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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701D PHE* 3.9 30.2 - + + -
703D THR* 5.0 4.0 - - - -
730D LEU* 4.2 24.9 - - + -
731D GLU* 4.8 6.5 - - + -
732D THR* 4.1 23.1 - - + -
745D LEU* 4.9 12.1 - - + -
748D CYS* 5.7 0.4 - - + -
749D ILE* 4.1 33.2 - - + -
752D MET* 4.5 7.9 - - - -
879D PRO* 3.1 33.0 - - + -
880D LEU* 3.7 20.0 - - + +
881D GLU 3.2 0.2 - - - -
882D GLY* 1.3 75.9 - - - +
884D THR* 1.3 64.9 + - - +
886D ALA* 3.1 5.1 + - - +
887D ALA* 3.0 23.0 + - - +
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Residues in contact with THR 884 (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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752D MET* 3.6 13.2 - - + -
760D LEU* 3.6 30.3 - - + -
880D LEU* 3.0 22.6 + - + +
881D GLU* 2.8 18.2 + - - +
883D PHE* 1.3 74.7 - - - +
885D SER* 1.3 68.7 + - - +
886D ALA 3.1 0.2 + - - -
887D ALA 3.2 1.9 + - - -
888D LYS 2.8 4.9 + - - -
889D LEU 2.7 42.7 + - - +
890D ASP* 4.9 0.2 - - - -
891D TYR* 3.7 24.1 - - + +
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Residues in contact with SER 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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881D GLU* 2.5 39.9 + - - -
882D GLY 3.6 3.6 - - - -
884D THR* 1.3 75.1 + - - +
886D ALA* 1.3 62.6 + - - +
888D LYS* 3.2 20.4 + - - +
889D LEU 4.7 4.3 - - - -
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Residues in contact with ALA 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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401D PRO* 5.0 5.6 - - + -
402D ASN* 3.2 24.8 - - - +
701D PHE* 4.4 10.8 - - + -
702D TRP 3.8 21.5 - - - +
703D THR* 4.5 10.5 - - + +
882D GLY 2.9 17.0 + - - +
883D PHE 3.5 4.7 - - - +
885D SER* 1.3 71.5 - - - +
887D ALA* 1.3 58.8 + - - +
888D LYS* 2.8 22.9 + - - +
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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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403D ARG* 2.6 47.0 + - + +
698D ILE* 3.3 34.8 - - + -
701D PHE* 4.3 7.1 - - + +
752D MET* 4.2 4.3 - - + -
883D PHE 3.0 15.5 + - - +
884D THR 4.0 2.5 - - - +
886D ALA* 1.3 73.2 - - - +
888D LYS* 1.3 59.7 + - - +
889D LEU* 3.3 11.8 + - + +
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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