Contacts of the helix formed by residues 792 - 804 (chain B) in PDB entry 6MZL
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 ASN 792 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335B ILE* 4.9 2.4 - - - +
747B TYR* 5.7 0.4 + - - -
790B SER* 2.5 22.5 + - - +
791B ASP* 1.3 72.3 - - - +
793B TYR* 1.3 82.6 + - + +
794B TYR* 3.1 2.7 - - - +
795B ARG* 3.1 19.9 + - - +
796B ALA* 3.2 9.0 + - - +
845B SER* 3.2 26.5 + - - +
846B TYR* 3.3 41.2 + - - +
849B THR* 4.9 5.4 - - - +
850B ILE* 3.4 15.2 - - - +
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Residues in contact with TYR 793 (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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335B ILE* 4.1 16.6 + - + +
336B ILE 5.5 0.2 - - - -
337B ASP* 3.0 50.9 - - + +
338B GLU* 4.6 6.8 + - - +
747B TYR* 3.6 16.2 + - - +
751B LYS* 3.6 14.6 - - - +
790B SER 5.5 0.9 - - - -
792B ASN* 1.3 92.1 - - + +
794B TYR* 1.3 61.2 + - - +
796B ALA* 3.0 10.8 + - + +
797B GLU* 2.9 34.2 + - - +
846B TYR* 3.1 31.7 + + - -
847B ARG* 5.2 3.8 + - - -
849B THR* 4.0 26.5 - - + -
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Residues in contact with TYR 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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723B PHE* 5.4 5.4 - - - -
737B LYS 6.1 0.9 - - - -
741B PHE* 4.7 22.4 - + + -
747B TYR* 4.7 7.9 + + + -
750B GLN* 3.1 61.8 + - + +
751B LYS* 3.9 16.5 - - + +
754B PRO* 5.5 1.4 - - + +
778B LEU* 5.1 12.7 - - - +
782B ASN* 4.4 14.4 - - - -
791B ASP* 5.0 7.2 - - + -
792B ASN 4.2 6.7 - - - +
793B TYR* 1.3 78.9 - - - +
795B ARG* 1.3 61.8 + - + +
797B GLU* 3.4 1.4 + - - +
798B MET* 3.0 60.4 + - + +
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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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782B ASN* 4.7 19.5 - - - +
791B ASP* 3.0 32.6 + - + +
792B ASN* 3.1 7.4 + - - +
794B TYR* 1.3 77.4 - - + +
796B ALA* 1.3 57.1 + - - +
798B MET* 3.4 10.8 + - - +
799B ILE* 2.9 36.8 + - + +
836B PHE* 3.9 28.3 - - + -
839B MET* 4.7 13.0 - - - +
840B GLU* 3.6 5.9 + - - -
843B LEU* 4.6 17.6 - - - +
845B SER* 3.6 16.0 + - - -
850B ILE* 3.4 32.7 - - + +
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Residues in contact with ALA 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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792B ASN* 3.2 4.5 + - - +
793B TYR* 3.0 22.0 + - + +
795B ARG* 1.3 81.0 - - - +
797B GLU* 1.3 67.6 + - - +
799B ILE* 3.3 7.2 + - - +
800B ASP* 2.9 28.2 + - - -
849B THR* 4.7 17.9 - - + -
850B ILE* 4.7 7.2 - - + -
853B SER* 3.8 20.5 + - - +
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Residues in contact with GLU 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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751B LYS* 3.3 49.4 - - + +
754B PRO* 5.6 1.1 - - - -
755B VAL* 3.3 19.0 - - + +
793B TYR* 2.9 16.8 + - - +
794B TYR 4.3 1.6 - - - +
796B ALA* 1.3 82.7 - - - +
798B MET* 1.3 61.4 + - - +
800B ASP* 3.1 30.3 - - - +
801B ALA* 2.8 22.9 + - - +
853B SER* 5.6 0.2 - - - -
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Residues in contact with MET 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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751B LYS 6.0 0.4 - - - +
754B PRO* 4.4 19.7 - - + -
775B ILE* 4.4 5.5 - - + +
778B LEU* 3.4 47.3 - - + +
779B ILE* 3.6 23.8 - - + +
782B ASN* 4.1 10.8 - - - +
794B TYR* 3.0 56.8 + - + +
795B ARG* 3.7 7.4 - - - +
797B GLU* 1.3 76.6 - - - +
799B ILE* 1.3 61.1 + - + +
801B ALA* 3.2 9.6 + - - +
802B LEU* 3.0 27.9 + - - +
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Residues in contact with ILE 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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779B ILE* 5.8 1.1 - - + -
795B ARG 2.9 19.7 + - - +
796B ALA 3.3 6.5 - - - +
798B MET* 1.3 77.3 - - + +
800B ASP* 1.3 57.0 + - - +
802B LEU* 3.0 20.4 + - + +
803B ALA* 2.8 23.2 + - - +
832B GLU 6.2 0.2 - - - -
833B ILE* 4.9 8.5 - - + -
836B PHE* 3.7 43.3 - - + -
850B ILE* 3.7 21.3 - - + -
853B SER* 3.4 35.0 - - - +
854B CYS* 4.0 11.2 - - - +
857B ALA* 4.7 5.5 - - + +
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Residues in contact with ASP 800 (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* 4.4 5.5 - - + +
796B ALA 2.9 13.7 + - - +
797B GLU* 3.1 39.0 + - - +
799B ILE* 1.3 72.9 - - - +
801B ALA* 1.3 55.9 + - - +
803B ALA* 3.1 11.4 + - + +
804B ASN* 2.7 33.3 + - - +
853B SER* 3.3 31.8 - - - +
856B ARG* 5.0 13.6 + - - +
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Residues in contact with ALA 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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754B PRO* 3.6 27.8 - - + +
755B VAL* 3.7 13.8 - - + +
758B ALA* 3.3 16.1 - - + +
775B ILE* 4.3 9.9 - - + -
797B GLU 2.8 13.6 + - - +
798B MET* 3.2 13.4 + - - +
800B ASP* 1.3 74.9 - - - +
802B LEU* 1.3 60.1 + - - +
804B ASN* 3.0 18.3 + - - +
805B SER* 3.1 10.4 + - - -
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Residues in contact with LEU 802 (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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772B LEU* 5.4 6.3 - - + +
775B ILE* 3.8 22.7 - - + -
776B LEU* 4.5 6.5 - - + -
779B ILE* 3.7 11.7 - - + -
798B MET 3.0 16.2 + - - +
799B ILE* 3.0 19.8 + - + +
801B ALA* 1.3 78.4 - - - +
803B ALA* 1.3 58.1 + - - +
805B SER* 2.3 31.6 + - - +
829B ILE* 3.8 38.3 - - + +
832B GLU* 3.3 31.6 - - + +
833B ILE* 5.0 6.1 - - + -
857B ALA* 5.5 0.9 - - + -
861B LEU* 5.8 2.6 - - - +
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Residues in contact with ALA 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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799B ILE 2.8 9.6 + - - +
800B ASP* 3.1 18.4 + - + +
802B LEU* 1.3 77.0 - - - +
804B ASN* 1.3 57.7 + - - +
805B SER 3.2 1.1 + - - -
806B VAL* 3.3 19.9 + - - +
856B ARG* 4.9 2.9 - - + -
857B ALA* 3.7 36.7 - - + +
860B VAL* 3.6 17.2 - - + +
861B LEU* 6.5 0.9 - - - -
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Residues in contact with ASN 804 (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* 3.9 16.5 - - + +
758B ALA* 3.0 15.3 - - + +
759B LEU* 3.3 42.6 - - - +
761B ARG* 2.4 29.0 + - - -
800B ASP 2.7 18.3 + - - +
801B ALA* 3.0 12.9 + - - +
803B ALA* 1.3 73.4 - - - +
805B SER* 1.3 49.2 + - - -
806B VAL* 3.2 11.0 - - - +
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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