Contacts of the helix formed by residues 802 - 816 (chain B) 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 802 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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786B ASN 6.0 0.4 - - - +
791B TYR* 3.5 24.2 - - + -
800B LYS 3.2 9.2 - - - +
801B CYS* 1.3 85.4 - - + +
803B PHE* 1.3 53.3 + - - +
804B HIS* 3.2 15.0 - - + -
805B ILE* 2.8 27.9 + - + -
806B ARG* 2.7 33.0 + - - +
10G A 5.5 0.4 - - - +
11G C 6.2 0.9 - - - -
110H A 3.9 31.4 - - - +
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Residues in contact with PHE 803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801B CYS 3.4 2.6 + - - -
802B PRO* 1.3 69.0 - - - +
804B HIS* 1.3 63.8 + - + +
806B ARG* 3.4 4.8 + - - +
807B GLY 3.2 16.5 + - - -
832B VAL* 4.3 20.0 - - + -
834B PRO* 4.8 15.3 - - + -
844B LYS* 3.9 27.1 - - + -
845B CYS* 3.4 37.5 - - + -
870B VAL* 6.3 1.3 - - + -
10G A 3.9 48.7 + - - +
11G C 3.7 19.8 + - - -
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Residues in contact with HIS 804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783B SER* 3.3 25.0 + - - +
784B SER 2.7 32.8 + - - -
785B ALA* 4.0 8.7 - - + -
802B PRO* 3.7 20.2 - - + +
803B PHE* 1.3 80.6 + - + +
805B ILE* 1.3 72.0 + - + +
807B GLY* 3.4 2.3 + - - +
808B ILE* 3.3 23.9 + - - +
830B VAL* 4.5 2.9 - - + +
832B VAL* 3.9 27.8 - - + -
847B ALA* 3.9 4.7 - - - +
110H A 3.5 11.9 - - - -
111H T 2.8 22.6 + - - -
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Residues in contact with ILE 805 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785B ALA* 3.8 32.5 - - + -
786B ASN 3.9 18.4 - - - +
787B ASN 5.2 0.4 - - - +
788B ILE* 3.9 22.9 - - + +
791B TYR* 3.9 17.9 - - + -
801B CYS* 3.9 13.7 - - - -
802B PRO* 2.8 31.4 + - + +
804B HIS* 1.3 88.8 - - + +
806B ARG* 1.3 66.4 + - - +
807B GLY 3.2 0.4 - - - -
808B ILE* 3.2 13.6 + - + +
809B LEU* 3.1 29.8 - - + +
111H T 4.6 0.2 - - - +
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Residues in contact with ARG 806 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797B PRO* 3.1 41.1 - - + +
798B GLY 5.5 1.2 + - - -
801B CYS* 3.7 22.2 + - - +
802B PRO 2.7 10.6 + - - +
803B PHE* 3.5 9.2 - - - +
805B ILE* 1.3 79.1 - - - +
807B GLY* 1.3 60.8 - - - +
809B LEU* 3.3 10.3 + - - +
810B THR* 3.2 19.9 + - - -
843B ASP* 3.4 32.4 + - - +
844B LYS* 3.6 29.3 - - - +
845B CYS* 4.2 7.9 - - - -
11G C 3.4 27.6 + - - -
12G A 5.4 7.3 + - - -
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Residues in contact with GLY 807 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803B PHE 3.2 7.9 + - - -
804B HIS* 3.4 4.7 + - - -
805B ILE 3.2 0.2 - - - -
806B ARG* 1.3 78.3 - - - +
808B ILE* 1.3 63.6 + - - +
810B THR* 3.2 4.0 + - - -
811B TYR* 3.1 17.8 + - - +
832B VAL* 5.5 0.2 - - - -
845B CYS* 3.6 27.6 - - - -
846B ILE 4.1 0.2 - - - -
847B ALA* 3.1 25.1 + - - -
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Residues in contact with ILE 808 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785B ALA* 3.1 37.9 - - + -
788B ILE* 3.5 31.0 - - + -
804B HIS 3.3 12.1 + - - +
805B ILE* 3.2 16.0 + - + +
807B GLY* 1.3 77.3 - - - +
809B LEU* 1.3 57.6 + - - +
811B TYR* 3.1 8.2 + - - +
812B ASN* 2.9 48.9 + - - +
824B VAL* 3.6 26.5 - - + -
830B VAL* 3.9 5.8 - - + -
847B ALA* 3.7 14.8 - - + +
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Residues in contact with LEU 809 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788B ILE* 3.9 28.5 - - + +
791B TYR 3.6 18.2 - - - +
792B ASP* 4.2 11.4 - - - +
795B GLY* 3.4 18.3 - - - +
796B PHE 3.6 27.1 - - - +
797B PRO* 3.6 10.3 - - + -
801B CYS* 4.4 5.8 - - - -
805B ILE* 3.1 21.0 + - + +
806B ARG* 3.6 6.7 - - - +
807B GLY 3.2 0.4 - - - -
808B ILE* 1.3 76.3 - - + +
810B THR* 1.3 65.7 + - - +
812B ASN* 3.1 11.3 + - - +
813B ARG* 3.0 32.5 + - - +
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Residues in contact with THR 810 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806B ARG 3.2 9.9 + - - -
807B GLY 3.2 5.5 + - - -
809B LEU* 1.3 75.6 - - - +
811B TYR* 1.3 57.4 + - - +
813B ARG* 3.6 13.5 + - - +
814B ALA* 3.0 24.9 + - - +
841B PHE* 3.3 42.8 - - + +
843B ASP* 2.9 22.0 + - + +
845B CYS 2.9 28.6 + - - +
846B ILE* 3.8 10.1 - - + -
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Residues in contact with TYR 811 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807B GLY 3.1 4.7 + - - +
808B ILE 3.3 7.4 - - - +
809B LEU 3.1 0.2 - - - -
810B THR* 1.3 78.8 - - - +
812B ASN* 1.3 71.8 + - - +
814B ALA* 3.1 3.4 + - - +
815B ILE* 3.1 50.9 + - + +
822B PRO* 2.6 44.8 + - - +
824B VAL* 3.6 33.2 - - + -
846B ILE* 3.7 11.6 - - + +
847B ALA 3.0 23.1 - - - +
848B TRP* 4.1 10.9 - - + +
849B PRO* 3.9 9.4 - - + +
854B ILE* 4.5 1.1 - - + -
855B THR* 3.9 19.5 + - + +
858B ILE* 3.8 17.9 - - + -
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Residues in contact with ASN 812 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788B ILE* 4.6 5.1 - - - +
792B ASP* 5.0 6.0 + - - +
795B GLY* 6.1 3.8 - - - -
808B ILE* 2.9 41.6 + - - +
809B LEU* 3.1 16.1 + - - +
811B TYR* 1.3 85.4 - - - +
813B ARG* 1.3 58.0 + - + +
815B ILE* 3.4 7.4 + - - +
816B LYS* 2.8 31.8 + - - +
823B GLN* 4.1 15.0 + - - +
824B VAL* 4.6 6.8 + - - +
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Residues in contact with ARG 813 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794B GLY 5.2 1.3 - - - +
795B GLY* 2.7 55.3 + - - +
796B PHE* 3.8 38.8 - - + +
797B PRO* 4.1 0.4 - - - +
809B LEU* 3.0 25.2 + - - +
810B THR* 3.6 18.4 + - - +
812B ASN* 1.3 77.6 - - - +
814B ALA* 1.3 62.6 + - - +
815B ILE 3.3 0.7 + - - -
816B LYS* 3.6 16.2 + - + +
841B PHE 3.3 25.0 + - - +
842B GLY* 4.4 4.2 - - - -
843B ASP* 3.4 27.1 + - - +
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Residues in contact with ALA 814 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810B THR 3.0 19.5 + - - +
811B TYR* 3.1 10.7 + - - +
813B ARG* 1.3 78.1 - - - +
815B ILE* 1.3 58.4 + - - +
841B PHE* 3.7 32.5 - - + -
857B LEU* 5.6 1.4 - - - +
858B ILE* 3.9 20.8 - - + +
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Residues in contact with ILE 815 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811B TYR* 3.1 50.8 + - + +
812B ASN* 3.8 4.7 - - - +
814B ALA* 1.3 83.0 - - + +
816B LYS* 1.3 70.4 + - - +
817B GLY 3.1 1.4 + - - -
818B ASN* 3.0 25.3 + - - +
821B ALA* 3.5 33.7 - - + +
822B PRO 3.9 3.4 - - - +
823B GLN* 3.1 31.0 - - - +
855B THR* 4.2 9.2 - - + -
857B LEU* 4.5 8.5 - - + -
858B ILE* 4.7 4.3 - - + -
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Residues in contact with LYS 816 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812B ASN 2.8 18.3 + - - +
813B ARG* 3.6 16.3 + - + +
815B ILE* 1.3 77.6 - - - +
817B GLY* 1.3 60.2 + - - +
818B ASN* 4.8 0.3 - - - +
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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
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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