Contacts of the helix formed by residues 802 - 815 (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 PRO 802 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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791D TYR* 3.1 31.4 - - + +
800D LYS 4.3 2.7 - - - +
801D CYS* 1.4 83.8 - - - +
803D PHE* 1.3 56.2 + - - +
804D HIS* 3.1 26.0 - - + -
805D ILE* 2.5 47.8 + - + +
806D ARG* 2.9 8.8 + - - -
10K A 4.5 4.9 - - - -
111L T 4.4 20.2 - - - +
112L T 5.2 0.7 - - - +
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Residues in contact with PHE 803 (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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801D CYS 3.7 3.2 + - - -
802D PRO* 1.3 70.0 - - - +
804D HIS* 1.3 64.4 + - + +
806D ARG* 3.3 11.9 - - - +
807D GLY 3.2 6.1 + - - -
832D VAL* 3.8 18.2 - - + -
833D LEU 5.6 0.2 - - - -
834D PRO* 4.7 13.0 - - + -
844D LYS* 3.8 41.7 - - + -
845D CYS* 2.9 61.7 - - + -
874D LYS* 6.1 2.2 - - - -
9K G 3.4 47.6 + - - +
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Residues in contact with HIS 804 (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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783D SER* 3.9 23.6 + - - +
784D SER 3.5 20.4 + - - -
802D PRO* 2.8 27.3 + - + +
803D PHE* 1.3 81.7 + - + +
805D ILE* 1.3 69.8 + - + +
806D ARG 3.1 1.1 - - - -
807D GLY* 3.3 2.0 + - - +
808D ILE* 2.9 34.8 + - + +
830D VAL* 5.9 0.7 - - + -
832D VAL* 4.1 24.5 - - + -
847D ALA* 4.1 2.4 - - - +
111L T 4.1 7.4 - - - -
112L T 3.0 32.4 + - - -
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Residues in contact with ILE 805 (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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785D ALA 4.4 1.1 - - - -
786D ASN 3.1 35.0 - - - +
787D ASN 4.6 4.5 - - - +
788D ILE* 4.4 17.3 - - + +
791D TYR* 4.0 18.8 - - + -
801D CYS* 3.7 15.5 - - - -
802D PRO* 2.5 41.1 + - + +
804D HIS* 1.3 88.3 - - + +
806D ARG* 1.3 64.3 + - - +
808D ILE* 3.1 12.4 + - + +
809D LEU* 3.0 26.8 + - + +
112L T 3.9 1.6 - - - +
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Residues in contact with ARG 806 (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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797D PRO* 3.3 29.3 - - + +
801D CYS* 3.3 24.9 + - - +
802D PRO 2.9 14.1 + - - +
803D PHE* 3.3 22.4 - - - +
805D ILE* 1.3 78.3 - - - +
807D GLY* 1.3 62.4 + - - +
808D ILE 3.0 0.7 + - - -
809D LEU* 3.1 3.2 + - - +
810D THR* 2.8 29.2 + - - -
843D ASP* 2.7 39.2 + - - +
844D LYS* 4.3 20.4 - - - +
845D CYS* 4.0 1.8 - - - -
10K A 3.7 16.9 + - - -
11K C 5.8 2.0 + - - -
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Residues in contact with GLY 807 (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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803D PHE 3.2 7.7 + - - -
804D HIS* 3.3 5.3 + - - -
805D ILE 3.3 0.4 - - - -
806D ARG* 1.3 79.3 - - - +
808D ILE* 1.3 59.9 + - - +
810D THR 4.0 0.2 - - - -
811D TYR 3.2 14.6 + - - -
832D VAL* 5.5 0.7 - - - -
845D CYS* 3.2 29.3 - - - -
846D ILE* 3.3 9.3 - - - -
847D ALA* 2.8 22.7 + - - -
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Residues in contact with ILE 808 (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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785D ALA* 3.2 38.4 - - + -
788D ILE* 3.6 13.9 - - + -
804D HIS* 2.9 28.7 + - + +
805D ILE* 3.3 19.7 - - + +
806D ARG 3.0 0.4 - - - -
807D GLY* 1.3 74.5 - - - +
809D LEU* 1.3 56.2 + - - +
811D TYR* 3.2 5.9 + - - +
812D ASN* 2.5 49.5 + - - +
824D VAL* 3.3 24.2 - - + -
830D VAL* 3.9 10.5 - - + -
847D ALA* 3.7 20.0 - - + -
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Residues in contact with LEU 809 (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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788D ILE* 3.3 29.6 - - + +
791D TYR 3.5 25.8 - - - +
792D ASP* 3.8 28.0 - - - +
795D GLY* 3.9 12.8 - - - +
796D PHE* 3.6 21.3 - - - +
797D PRO* 3.9 9.0 - - + -
801D CYS* 4.7 1.8 - - - -
805D ILE* 3.0 23.9 + - + +
806D ARG* 3.7 4.3 - - - +
808D ILE* 1.3 72.4 - - - +
810D THR* 1.3 65.2 + - - +
812D ASN* 3.1 12.3 + - + +
813D ARG* 3.0 31.1 + - - +
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Residues in contact with THR 810 (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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806D ARG 2.8 19.8 + - - -
807D GLY 3.6 2.5 - - - -
809D LEU* 1.3 77.2 - - - +
811D TYR* 1.3 63.9 + - - +
813D ARG* 3.3 18.6 - - - +
814D ALA* 3.0 21.8 + - - +
841D PHE* 3.6 40.7 - - + +
843D ASP* 2.9 29.2 + - + +
845D CYS 3.5 20.4 + - - +
846D ILE* 4.7 4.7 - - + -
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Residues in contact with TYR 811 (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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807D GLY 3.2 6.4 + - - +
808D ILE 3.3 5.6 - - - +
810D THR* 1.3 80.9 - - - +
812D ASN* 1.3 65.9 + - - +
814D ALA* 2.7 30.7 + - - +
815D ILE* 3.1 25.9 + - + +
821D ALA 4.8 0.3 - - - -
822D PRO* 3.0 31.9 + - - +
823D GLN* 4.6 0.2 - - - -
824D VAL* 4.0 12.3 - - + -
846D ILE* 3.6 16.6 - - + +
847D ALA 3.2 26.5 - - - +
848D TRP* 3.8 16.4 - + + +
849D PRO* 3.9 13.8 - - + +
854D ILE* 4.6 3.1 - - + -
855D THR* 4.0 16.5 + - - -
858D ILE* 3.3 32.8 - - + -
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Residues in contact with ASN 812 (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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788D ILE* 4.2 7.1 - - - +
808D ILE* 2.5 48.4 + - - +
809D LEU* 3.1 16.3 + - + +
811D TYR* 1.3 79.0 - - - +
813D ARG* 1.3 56.8 + - - +
815D ILE* 3.5 1.3 + - - +
816D LYS* 3.0 23.6 + - - +
823D GLN* 3.1 34.6 + - - +
824D VAL* 2.9 29.1 + - - +
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Residues in contact with ARG 813 (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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795D GLY* 3.6 21.4 + - - +
796D PHE* 3.8 38.4 - - - -
797D PRO* 4.2 8.9 - - - +
809D LEU 3.0 9.0 + - - +
810D THR* 3.3 37.3 + - - +
812D ASN* 1.3 74.4 - - - +
814D ALA* 1.3 63.8 + - - +
815D ILE 3.2 1.2 + - - -
816D LYS* 3.5 21.4 + - + +
841D PHE 3.2 24.5 + - - +
842D GLY* 3.8 9.7 + - - -
843D ASP* 3.0 26.3 + - - -
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Residues in contact with ALA 814 (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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810D THR 3.0 15.0 + - - +
811D TYR* 2.7 18.8 + - - +
813D ARG* 1.3 79.5 - - - +
815D ILE* 1.3 61.3 + - + +
841D PHE* 4.2 24.2 - - + +
846D ILE* 4.8 1.6 - - + -
857D LEU* 6.0 0.5 - - - +
858D ILE* 4.3 18.0 - - + +
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Residues in contact with ILE 815 (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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811D TYR* 3.1 32.5 + - + +
812D ASN 3.7 1.3 - - - +
814D ALA* 1.3 80.7 - - - +
816D LYS* 1.3 53.3 - - - +
817D GLY 2.8 17.7 + - - -
818D ASN* 3.3 23.4 + - - +
821D ALA* 3.8 32.8 - - + +
823D GLN* 3.2 38.6 - - - +
855D THR* 5.4 1.8 - - - -
857D LEU* 4.6 13.2 - - + -
858D ILE* 3.9 29.8 - - + -
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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