Contacts of the helix formed by residues 789 - 801 (chain B) in PDB entry 5J3V
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 MET 789 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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751B LEU* 3.6 27.1 - - + +
752B HIS* 5.3 14.1 - - - -
755B VAL* 5.6 9.0 - - + -
785B GLU 3.3 25.6 - - - +
786B VAL* 3.1 8.4 + - + +
787B ALA 3.0 1.6 - - - -
788B PRO* 1.3 94.3 - - + +
790B LEU* 1.3 64.0 + - - +
791B GLN* 3.1 3.4 - - - -
792B GLN* 3.1 40.8 + - + +
793B PHE* 3.1 18.9 - - + -
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Residues in contact with LEU 790 (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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786B VAL 3.6 1.8 + - - -
787B ALA 2.9 16.8 + - - +
789B MET* 1.3 77.1 - - - +
791B GLN* 1.3 63.4 + - - +
792B GLN 3.3 0.5 + - - -
793B PHE* 3.5 13.4 + - + -
794B ILE* 3.2 54.2 + - + +
817B ILE* 3.7 13.2 - - + -
820B MET* 3.6 41.5 - - + +
821B ILE* 4.3 1.1 - - + +
824B ASN* 3.5 29.4 - - + +
827B GLY* 4.4 5.6 - - - -
828B VAL* 3.7 22.7 - - + -
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Residues in contact with GLN 791 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788B PRO 3.5 14.4 + - - +
789B MET 3.1 0.7 - - - -
790B LEU* 1.3 81.8 + - - +
792B GLN* 1.3 67.2 + - + +
793B PHE 3.6 0.2 - - - -
794B ILE* 3.9 11.0 - - - +
795B ARG* 5.3 1.7 + - - +
824B ASN* 3.0 27.7 + - - +
826B SER* 3.8 10.3 + - - +
827B GLY* 3.4 31.0 - - - +
830B GLN* 4.3 19.9 - - - +
831B ASP* 4.4 7.4 - - - +
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Residues in contact with GLN 792 (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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755B VAL* 4.0 18.1 - - + +
759B ASN* 3.0 24.0 + - - +
789B MET* 3.1 37.3 + - - +
791B GLN* 1.3 85.9 - - + +
793B PHE* 1.3 59.4 + - - +
794B ILE 3.7 0.2 - - - -
795B ARG* 4.9 3.7 + - - +
796B PRO* 4.6 1.6 - - - +
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Residues in contact with PHE 793 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751B LEU* 5.9 1.8 - - + -
755B VAL* 3.9 19.3 - - + -
758B ILE* 4.0 14.3 - - + +
759B ASN* 4.2 2.0 - - - +
775B ILE* 3.6 35.9 - - + -
776B GLY* 6.4 0.2 - - - -
786B VAL* 4.2 6.1 - - + -
789B MET* 3.1 31.4 - - + -
790B LEU* 3.5 21.1 - - + -
792B GLN* 1.3 78.9 - - - +
794B ILE* 1.3 60.4 + - - +
795B ARG 3.2 3.1 - - - -
796B PRO* 3.1 17.7 - - - +
797B TRP* 3.0 37.3 + + + +
817B ILE* 3.8 20.6 - - + -
820B MET* 3.5 28.3 - - + -
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Residues in contact with ILE 794 (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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790B LEU* 3.2 39.5 - - + +
791B GLN 3.9 9.9 - - - +
793B PHE* 1.3 81.6 - - + +
795B ARG* 1.3 67.8 + - - +
797B TRP* 3.7 7.2 - - + -
798B CYS* 3.3 35.9 + - - +
817B ILE* 4.5 8.7 - - + -
827B GLY 3.2 27.1 - - - +
828B VAL* 3.7 24.5 - - + +
831B ASP* 3.8 29.4 - - + +
834B PHE* 4.5 3.0 - - - +
835B PHE* 6.4 0.4 - - + -
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Residues in contact with ARG 795 (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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759B ASN* 5.0 2.2 - - - +
791B GLN 5.8 1.3 - - - +
792B GLN 5.1 4.7 - - - +
793B PHE 3.2 0.4 - - - +
794B ILE* 1.3 83.2 - - - +
796B PRO* 1.3 64.8 - - + +
799B THR* 3.3 23.0 - - - +
831B ASP* 3.0 31.6 + - - +
834B PHE* 3.2 44.5 - - + -
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Residues in contact with PRO 796 (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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758B ILE* 3.2 42.5 - - + +
759B ASN* 3.2 24.2 - - - +
768B LEU* 5.7 5.1 - - + +
793B PHE* 3.1 21.8 - - - +
795B ARG* 1.3 87.2 - - + +
797B TRP* 1.3 62.4 + - - +
798B CYS 3.3 0.9 - - - -
799B THR* 2.8 21.6 + - - +
800B SER* 3.1 16.3 + - - -
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Residues in contact with TRP 797 (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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758B ILE* 3.8 9.2 - - + -
772B ALA* 3.1 39.9 + - + -
775B ILE* 4.9 1.6 - - + -
776B GLY* 4.3 6.2 - - - +
793B PHE* 3.0 43.0 + + + +
794B ILE* 3.4 8.7 + - - -
796B PRO* 1.3 78.1 - - - +
798B CYS* 1.3 82.9 + - - +
800B SER* 3.8 0.7 - - - -
801B LEU* 3.2 45.2 + - + +
813B ALA* 3.4 23.1 - - + -
814B PHE* 4.0 31.9 - + - -
817B ILE* 3.6 41.7 - - + -
835B PHE* 5.6 2.0 - + - -
838B ALA* 4.7 0.2 - - + -
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Residues in contact with CYS 798 (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 ILE* 3.3 27.4 + - - +
797B TRP* 1.3 99.2 - - - +
799B THR* 1.3 64.1 + - - +
801B LEU 4.7 0.2 - - - +
802B ARG* 3.2 26.5 + - - +
817B ILE* 6.1 0.2 - - - -
831B ASP 5.7 0.4 - - - -
834B PHE* 3.2 26.9 - - + +
835B PHE* 3.7 33.2 - - - -
837B ASP* 5.2 1.7 - - + -
838B ALA* 3.8 13.5 + - + +
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Residues in contact with THR 799 (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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795B ARG 3.3 16.6 - - - +
796B PRO* 2.8 27.6 + - + +
798B CYS* 1.3 77.2 - - - +
800B SER* 1.3 60.3 + - - +
802B ARG* 4.0 25.3 + - - +
803B ASN* 4.0 14.4 + - - -
834B PHE* 3.5 27.6 - - + -
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Residues in contact with SER 800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758B ILE* 5.7 1.1 - - - -
768B LEU* 3.6 43.3 + - - +
769B GLU* 3.6 15.2 + - - +
772B ALA* 4.8 1.1 - - - -
796B PRO 3.1 18.4 + - - -
797B TRP* 3.8 5.2 - - - -
799B THR* 1.3 76.7 + - - +
801B LEU* 1.3 61.7 + - - +
802B ARG 3.1 8.6 + - - -
803B ASN* 3.6 12.8 + - - +
804B ILE* 3.9 10.4 - - - +
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Residues in contact with LEU 801 (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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769B GLU 4.0 9.4 - - - +
772B ALA* 3.7 24.5 - - + -
773B ILE* 4.3 5.8 - - + +
797B TRP* 3.2 52.3 + - + +
798B CYS 4.0 2.0 - - - +
800B SER* 1.3 77.1 - - - +
802B ARG* 1.3 60.8 + - - +
803B ASN 3.4 0.9 - - - -
804B ILE* 3.6 28.2 + - + -
810B LYS* 3.3 29.0 - - + +
813B ALA* 3.8 19.5 - - + -
814B PHE* 4.2 18.9 - - + -
841B SER* 4.1 4.0 + - - -
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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