Contacts of the helix formed by residues 756 - 773 (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 GLY 756 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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696D LYS* 2.7 31.0 + - - -
697D GLY* 3.5 1.0 - - - +
751D ARG 3.4 7.8 + - - -
752D MET* 4.8 4.0 + - - -
755D GLU* 1.3 78.3 - - - +
757D GLU* 1.3 52.4 + - - -
758D GLU* 2.4 22.5 + - - +
759D SER* 2.6 21.5 + - - -
760D LEU* 3.6 2.6 + - - -
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Residues in contact with GLU 757 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B GLY 5.6 1.6 - - - +
696D LYS* 4.1 3.0 + - - +
698D ILE* 5.9 0.4 - - - +
752D MET* 5.8 0.4 - - - +
756D GLY* 1.3 68.6 - - - -
758D GLU* 1.3 60.1 + - - +
760D LEU* 3.5 9.9 + - - +
761D GLN* 2.9 36.8 + - - +
888D LYS 4.7 0.5 - - - +
889D LEU* 3.4 41.1 - - + +
890D ASP* 2.9 54.8 + - - +
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Residues in contact with GLU 758 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696D LYS* 5.2 4.7 - - + -
755D GLU* 3.8 13.3 - - - +
756D GLY* 2.4 21.8 + - - +
757D GLU* 1.3 70.2 - - - +
759D SER* 1.3 89.8 + - - +
761D GLN* 2.8 17.0 + - - +
762D GLU* 2.8 31.3 + - - +
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Residues in contact with SER 759 (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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751D ARG* 2.9 34.2 + - - +
755D GLU* 2.5 38.5 + - - -
756D GLY 2.6 14.6 + - - -
758D GLU* 1.3 92.2 - - - +
760D LEU* 1.3 64.0 + - - -
762D GLU* 3.2 10.5 + - - -
763D TYR* 2.8 20.4 + - - +
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Residues in contact with LEU 760 (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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748D CYS* 3.9 43.7 - - + +
751D ARG* 4.5 6.9 - - + +
752D MET* 3.4 40.6 - - + +
756D GLY 3.6 2.9 + - - +
757D GLU* 3.5 12.3 + - - +
758D GLU 3.1 0.6 - - - -
759D SER* 1.3 78.9 - - - +
761D GLN* 1.3 58.8 + - - +
763D TYR* 3.1 5.4 + - + +
764D PHE* 2.8 28.7 + - + +
880D LEU* 4.4 10.5 - - + -
884D THR* 3.6 15.9 - - + -
889D LEU* 4.7 5.4 - - + -
890D ASP 4.2 13.5 - - - +
891D TYR* 4.1 9.2 - - + -
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Residues in contact with GLN 761 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757D GLU* 2.9 24.5 + - - +
758D GLU* 2.8 16.5 + - - +
760D LEU* 1.3 72.5 - - - +
762D GLU* 1.3 62.0 + - - +
764D PHE* 3.2 9.9 + - - +
765D LYS* 3.3 13.7 + - - +
890D ASP* 2.7 38.0 + - - +
891D TYR 3.2 18.3 - - - +
892D GLU 3.2 2.2 + - - -
893D LYS* 3.1 44.7 - - + +
894D LYS 4.4 1.4 - - - +
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Residues in contact with GLU 762 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751D ARG* 2.8 34.3 + - - -
758D GLU* 2.8 23.6 + - - +
759D SER* 3.4 13.7 + - - +
761D GLN* 1.3 73.8 - - - +
763D TYR* 1.3 61.5 + - - +
765D LYS* 3.6 4.2 + - - +
766D GLU* 3.1 25.2 + - + +
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Residues in contact with TYR 763 (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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743D LYS 4.4 0.5 + - - -
744D ALA* 3.6 36.1 - - + +
747D GLU* 3.3 29.6 - - + +
748D CYS* 4.0 23.8 - - - -
751D ARG* 2.8 42.0 - - - +
759D SER 2.8 12.9 + - - +
760D LEU* 3.5 4.0 - - + +
762D GLU* 1.3 73.2 - - - +
764D PHE* 1.3 65.3 + - - +
766D GLU* 3.4 27.7 - - + +
767D PHE* 3.0 37.8 + + + +
770D GLU* 5.0 2.8 + - - -
876D PHE* 5.3 1.1 - + - -
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Residues in contact with PHE 764 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748D CYS* 5.9 0.9 - - - -
760D LEU* 2.8 12.5 + - + +
761D GLN 3.2 9.4 + - - +
763D TYR* 1.3 79.8 - - - +
765D LYS* 1.3 73.4 + - + +
767D PHE* 3.2 4.7 + - - +
768D GLU* 3.2 42.6 + - + +
876D PHE* 3.4 35.5 - + - -
877D ILE* 4.3 17.0 - - + -
880D LEU* 3.8 20.6 - - + -
891D TYR* 3.4 52.0 - + + +
892D GLU* 5.1 4.9 - - + -
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Residues in contact with LYS 765 (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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761D GLN 3.3 8.8 + - - +
762D GLU* 4.0 6.1 - - - +
764D PHE* 1.3 82.2 - - + +
766D GLU* 1.3 64.0 + - - +
768D GLU* 2.9 30.5 + - - +
769D LYS* 3.5 4.2 + - - +
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Residues in contact with GLU 766 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751D ARG* 5.6 1.6 + - - +
762D GLU* 3.1 22.6 + - + +
763D TYR* 3.4 28.2 - - + +
765D LYS* 1.3 78.2 - - - +
767D PHE* 1.3 69.6 + - - +
769D LYS* 3.3 15.7 + - - +
770D GLU* 3.4 26.8 + - - +
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Residues in contact with PHE 767 (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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740D ALA* 4.2 19.3 - - + -
741D VAL* 4.4 4.3 - - + -
744D ALA* 3.6 27.8 - - + -
763D TYR* 3.0 33.9 + + + +
764D PHE 3.7 3.8 - - - +
766D GLU* 1.3 76.9 + - - +
768D GLU* 1.3 60.1 + - - +
769D LYS 2.9 2.2 + - - -
770D GLU* 3.1 26.4 + - + -
771D PHE* 2.6 65.7 + + + +
774D LEU* 4.7 9.6 - - + -
872D LEU* 4.3 7.9 - - + -
876D PHE* 3.9 33.7 - + + -
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Residues in contact with GLU 768 (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* 3.2 45.0 + - + +
765D LYS* 2.9 19.9 + - - +
767D PHE* 1.3 80.4 - - - +
769D LYS* 1.3 61.8 + - - +
771D PHE* 3.6 13.2 - - - +
772D ARG* 3.9 16.8 + - - +
872D LEU* 3.4 28.2 - - - +
876D PHE* 5.9 1.8 - - + -
877D ILE* 4.6 4.9 - - - +
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Residues in contact with LYS 769 (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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765D LYS 3.5 2.6 + - - +
766D GLU* 3.3 10.9 + - - +
767D PHE 2.9 1.2 + - - -
768D GLU* 1.3 79.4 - - - +
770D GLU* 1.3 57.1 + - - +
771D PHE 2.5 16.7 + - - -
772D ARG* 3.2 10.2 + - - +
773D GLN* 3.6 15.7 + - - +
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Residues in contact with GLU 770 (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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763D TYR* 5.0 3.3 + - - -
766D GLU* 3.4 22.7 + - - +
767D PHE* 3.1 31.8 + - - +
769D LYS* 1.3 78.3 - - - +
771D PHE* 1.3 59.3 + - - +
773D GLN* 3.6 17.8 + - + +
774D LEU* 2.9 47.6 + - + +
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Residues in contact with PHE 771 (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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740D ALA* 5.4 2.7 - - + -
741D VAL* 4.7 12.6 - - + -
767D PHE* 2.6 42.1 + + + +
768D GLU* 3.6 9.2 - - - +
769D LYS 2.5 4.8 + - - -
770D GLU* 1.3 66.1 - - - +
772D ARG* 1.3 70.1 + - + +
773D GLN 2.7 15.9 + - - -
774D LEU* 2.8 33.6 + - + +
779D ILE* 3.3 41.4 - - + +
868D TYR* 3.9 22.7 - + + -
871D LEU* 4.5 3.1 - - + -
872D LEU* 3.4 59.2 - - + -
875D THR* 5.7 0.4 - - - -
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Residues in contact with ARG 772 (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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768D GLU* 3.9 12.7 + - - +
769D LYS 3.2 5.8 + - - +
771D PHE* 1.3 80.8 - - - +
773D GLN* 1.3 57.7 + - - +
774D LEU 3.4 3.1 + - - +
868D TYR* 3.5 81.0 + - + +
869D THR* 4.9 10.5 + - - +
872D LEU* 4.6 15.4 - - - +
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Residues in contact with GLN 773 (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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769D LYS* 3.6 12.0 + - - +
770D GLU* 3.6 22.0 + - + +
771D PHE 2.7 4.4 + - - -
772D ARG* 1.3 76.0 - - - +
774D LEU* 1.3 60.9 + - - +
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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