Contacts of the helix formed by residues 738 - 755 (chain C) 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 PRO 738 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736C SER 3.9 5.6 - - - +
737C THR* 1.3 88.1 - - + +
739C LYS* 1.3 68.5 + - - +
741C VAL* 2.8 38.4 + - + -
742C GLN* 2.9 10.6 + - - +
778C SER 3.3 13.9 - - - +
779C ILE* 3.3 18.2 - - - +
780C ALA 3.0 27.8 - - - +
781C SER* 4.0 7.4 - - - +
782C VAL* 6.3 0.4 - - + -
875C THR* 4.0 18.6 - - + -
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Residues in contact with LYS 739 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C GLN* 5.8 1.5 - - - +
286C PRO* 4.1 17.9 - - + +
292C TYR* 3.7 24.1 + - - +
735C SER* 5.5 1.2 + - - +
737C THR 3.4 4.2 + - - +
738C PRO* 1.3 67.6 - - - +
740C ALA* 1.3 65.5 + - - +
742C GLN* 2.8 47.3 + - - +
743C LYS* 3.1 27.0 + - - +
777C ILE 5.3 1.7 + - - +
778C SER* 3.2 17.7 + - - +
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Residues in contact with ALA 740 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739C LYS* 1.3 74.4 - - - +
741C VAL* 1.3 56.8 + - - +
743C LYS* 3.4 14.0 + - - +
744C ALA* 3.0 25.8 + - - +
767C PHE* 4.1 5.8 - - + -
774C LEU* 3.8 26.9 - - + -
778C SER* 2.9 38.0 + - - +
779C ILE* 4.0 4.3 - - + -
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Residues in contact with VAL 741 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737C THR* 3.7 13.0 - - + -
738C PRO* 2.8 33.6 + - + +
740C ALA* 1.3 71.1 - - + +
742C GLN* 1.3 67.2 + - - +
743C LYS 3.0 1.8 - - - -
744C ALA* 3.7 4.8 - - - +
745C LEU* 2.8 35.5 + - + +
767C PHE* 4.4 14.8 - - + -
771C PHE* 4.6 10.8 - - + -
779C ILE* 5.3 1.3 - - - -
875C THR* 3.5 37.9 - - - +
876C PHE* 4.3 10.1 - - + -
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Residues in contact with GLN 742 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732C THR* 3.7 33.9 + - - +
733C GLN 5.0 0.8 - - - -
734C LYS 3.0 28.1 + - - -
735C SER* 4.3 5.5 - - - +
737C THR* 3.5 27.8 + - + -
738C PRO 2.9 13.7 + - - +
739C LYS* 2.8 40.8 + - - +
741C VAL* 1.3 71.5 - - - +
743C LYS* 1.3 60.0 + - + +
745C LEU* 4.7 0.2 - - - -
746C LYS* 2.8 32.1 + - - +
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Residues in contact with LYS 743 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739C LYS* 3.5 26.0 - - - +
740C ALA* 3.4 13.2 - - - +
741C VAL 3.0 0.2 - - - -
742C GLN* 1.3 79.3 - - + +
744C ALA* 1.3 57.4 + - - +
746C LYS* 3.0 8.5 + - - +
747C GLU* 2.8 29.4 + - - +
763C TYR* 4.9 0.4 - - - -
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Residues in contact with ALA 744 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740C ALA 3.0 9.5 + - - +
741C VAL 3.2 3.3 + - - +
743C LYS* 1.3 75.8 - - - +
745C LEU* 1.3 57.3 + - - +
747C GLU 3.2 1.2 + - - -
748C CYS* 2.8 25.6 + - - +
763C TYR* 3.5 25.0 + - + +
767C PHE* 3.5 39.3 - - + -
876C PHE* 3.6 19.7 - - + -
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Residues in contact with LEU 745 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731C GLU* 4.2 15.3 - - + -
732C THR* 3.4 18.4 - - + +
737C THR* 5.2 0.7 - - + -
741C VAL* 2.8 32.5 + - + +
744C ALA* 1.3 70.9 - - - +
746C LYS* 1.3 61.7 + - - +
748C CYS* 3.4 4.1 - - + +
749C ILE* 2.9 33.6 + - - +
875C THR 4.3 0.4 - - - +
876C PHE* 3.6 36.6 - - + +
879C PRO* 3.9 23.3 - - + -
880C LEU* 4.0 11.9 - - + -
883C PHE* 3.8 28.9 - - + -
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Residues in contact with LYS 746 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725C LEU* 3.6 40.5 + - + +
727C ILE* 4.3 15.7 - - + -
732C THR* 3.7 11.2 - - + +
733C GLN* 5.6 1.1 - - - +
742C GLN 2.8 19.3 + - - +
743C LYS* 3.2 9.2 - - - +
745C LEU* 1.3 76.0 - - - +
747C GLU* 1.3 59.0 + - - +
749C ILE* 3.4 1.4 + - - +
750C ARG* 3.0 24.5 + - + +
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Residues in contact with GLU 747 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743C LYS 2.8 12.3 + - - +
744C ALA 3.6 7.4 - - - +
746C LYS* 1.3 77.4 - - - +
748C CYS* 1.3 64.0 + - - +
750C ARG* 2.7 44.1 + - - -
751C ARG* 2.8 40.1 + - - +
763C TYR* 3.9 34.1 - - + +
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Residues in contact with CYS 748 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744C ALA 2.8 16.5 + - - +
745C LEU* 3.2 12.3 + - + +
747C GLU* 1.3 77.6 - - - +
749C ILE* 1.3 59.5 + - + +
751C ARG* 3.2 4.9 + - - +
752C MET* 2.8 32.9 + - - +
760C LEU* 3.5 30.3 - - + +
763C TYR* 4.0 16.6 - - - -
764C PHE* 5.3 2.2 - - - -
876C PHE* 4.1 11.0 - - - -
880C LEU* 3.7 31.9 - - + -
883C PHE* 5.5 0.4 - - + -
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Residues in contact with ILE 749 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701C PHE* 4.1 6.7 - - + -
709C ALA* 3.4 24.0 - - + -
725C LEU* 4.3 3.1 - - + -
727C ILE* 3.4 31.4 - - + -
730C LEU* 3.4 30.1 - - + -
732C THR* 4.4 5.8 - - + -
745C LEU 2.9 20.3 + - - +
746C LYS 3.8 3.8 - - - +
748C CYS* 1.3 75.0 - - - +
750C ARG* 1.3 63.9 + - - +
752C MET* 3.4 7.4 - - - +
753C LEU* 2.9 34.4 + - + +
883C PHE* 4.1 21.8 - - + -
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Residues in contact with ARG 750 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725C LEU* 3.6 26.9 - - + +
746C LYS* 3.0 11.2 + - + +
747C GLU* 2.7 43.0 + - - +
748C CYS 3.2 0.2 - - - -
749C ILE* 1.3 76.6 - - - +
751C ARG* 1.3 77.4 + - - +
754C GLN* 2.7 86.4 + - - +
755C GLU* 3.1 32.5 + - - +
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Residues in contact with ARG 751 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747C GLU* 2.8 34.6 + - - +
748C CYS* 3.7 4.3 - - - +
750C ARG* 1.3 92.6 - - - +
752C MET* 1.3 58.8 + - - +
755C GLU* 2.9 12.2 + - - +
756C GLY* 2.7 33.8 + - - +
759C SER* 3.1 50.6 + - - +
760C LEU* 4.2 8.3 - - - +
762C GLU* 4.2 6.5 - - - +
763C TYR* 3.6 35.4 - - - +
766C GLU* 5.2 5.3 + - - -
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Residues in contact with MET 752 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698C ILE* 3.4 25.9 + - + +
701C PHE* 3.7 25.8 - - + -
748C CYS 2.8 17.3 + - - +
749C ILE* 3.4 10.3 - - - +
751C ARG* 1.3 80.5 - - - +
753C LEU* 1.3 64.5 + - + +
756C GLY* 3.9 10.6 + - - +
760C LEU* 3.6 18.6 - - + +
880C LEU* 4.9 3.8 - - - -
883C PHE* 3.7 27.6 - - - +
884C THR* 4.0 14.6 - - - +
887C ALA* 3.6 31.0 - - + -
889C LEU* 3.3 22.6 - - + +
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Residues in contact with LEU 753 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691C PRO* 3.8 6.2 - - - +
697C GLY* 3.2 8.4 - - - -
698C ILE* 3.8 6.7 - - + -
699C GLY* 3.1 30.7 + - - +
700C GLY* 3.5 23.6 - - - +
701C PHE* 3.6 24.7 - - + -
709C ALA 3.8 3.1 - - - -
710C LEU* 3.6 41.7 - - - +
711C ASN* 3.6 9.9 - - + +
725C LEU* 3.8 15.7 - - + -
749C ILE* 2.9 26.0 + - + +
750C ARG 4.1 1.6 - - - +
752C MET* 1.3 79.8 - - + +
754C GLN* 1.3 59.3 + - + +
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Residues in contact with GLN 754 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692C PRO* 3.8 19.0 - - + +
695C SER* 3.7 23.2 + - - -
697C GLY* 3.8 3.4 - - - -
711C ASN* 2.5 37.8 - - - +
723C PRO* 3.8 24.3 + - - +
725C LEU* 4.3 4.8 - - - +
750C ARG* 2.7 67.8 + - + +
753C LEU* 1.3 75.9 - - + +
755C GLU* 1.3 65.2 + - + +
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Residues in contact with GLU 755 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695C SER* 5.4 0.9 - - - -
696C LYS* 3.6 19.1 + - - +
697C GLY 4.1 5.2 - - - -
750C ARG* 3.1 38.3 + - - +
751C ARG* 2.9 10.7 + - - +
754C GLN* 1.3 83.9 - - + +
756C GLY* 1.3 61.6 + - - +
759C SER* 2.7 39.3 + - - +
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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
------------------------------------------------------------
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