Contacts of the helix formed by residues 802 - 815 (chain A) in PDB entry 5M64
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 GLY 802 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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797A LEU 3.3 0.9 + - - +
798A HIS* 3.2 20.3 + - - +
799A GLU 4.5 1.3 - - - -
801A TYR* 1.3 78.5 - - - +
803A PRO* 1.3 71.2 - - - +
804A GLU 3.4 1.8 - - - -
805A VAL* 3.6 3.3 + - - -
806A ALA* 2.9 28.8 + - - +
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Residues in contact with PRO 803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654A ASP* 3.5 38.0 - - + +
655A SER* 5.2 4.0 - - - +
657A TYR* 5.5 1.2 - - + +
798A HIS* 3.4 32.5 - - + +
802A GLY* 1.3 80.7 - - - +
804A GLU* 1.3 61.7 + - + +
806A ALA* 3.3 1.6 + - - +
807A ALA* 2.9 28.9 + - - +
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Residues in contact with GLU 804 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654A ASP* 4.1 15.8 + - - +
802A GLY 3.4 0.4 - - - -
803A PRO* 1.3 82.5 - - + +
805A VAL* 1.3 75.8 + - + +
807A ALA* 3.4 5.4 + - - +
808A LYS* 2.9 41.7 + - - +
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Residues in contact with VAL 805 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A VAL 5.1 9.6 - - - +
741A PRO* 5.5 6.3 - - + -
797A LEU* 5.8 0.2 - - - -
801A TYR* 3.6 53.4 - - + +
802A GLY* 3.6 2.2 + - - +
803A PRO 3.3 0.4 - - - -
804A GLU* 1.3 88.9 - - + +
806A ALA* 1.3 61.4 + - - +
808A LYS* 3.9 10.8 - - + -
809A VAL* 2.8 39.9 + - + +
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Residues in contact with ALA 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657A TYR* 5.7 5.8 - - + -
667A ARG* 5.1 0.6 + - - -
794A VAL* 4.2 13.1 - - + +
797A LEU* 4.7 3.8 + - - -
798A HIS* 3.8 31.6 - - + +
802A GLY 2.9 19.4 + - - +
803A PRO 3.3 5.4 + - - +
805A VAL* 1.3 77.4 - - - +
807A ALA* 1.3 57.9 + - - +
809A VAL* 3.2 12.1 - - - +
810A LEU* 3.1 31.2 + - - +
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Residues in contact with ALA 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491A GLU* 5.3 5.2 - - - +
492A THR* 3.7 20.5 + - + +
493A ASN* 5.9 2.9 - - - +
653A THR* 5.7 5.2 - - + -
654A ASP* 5.0 10.5 - - + -
667A ARG* 4.7 7.0 - - - +
803A PRO 2.9 15.8 + - - +
804A GLU* 3.8 6.5 - - - +
806A ALA* 1.3 76.6 - - - +
808A LYS* 1.3 51.6 + - - +
810A LEU* 3.8 4.4 - - - -
811A SER* 2.3 38.0 + - - +
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Residues in contact with LYS 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491A GLU* 5.3 6.5 - - - +
705A GLY 2.9 24.6 + - - -
706A HIS* 3.2 43.9 + - + +
739A VAL* 4.3 15.5 - - + +
804A GLU* 2.9 35.1 + - - +
805A VAL* 3.1 12.1 + - + +
807A ALA* 1.3 76.1 - - - +
809A VAL* 1.3 61.6 + - - +
810A LEU 3.2 0.2 - - - -
811A SER* 3.0 20.5 + - - -
812A VAL* 3.1 16.0 + - - +
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Residues in contact with VAL 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736A LEU* 4.4 4.0 - - + -
739A VAL* 3.6 33.4 - - + -
794A VAL* 5.7 0.9 - - - -
797A LEU* 3.7 33.9 - - + -
801A TYR* 5.1 2.2 - - + -
805A VAL* 2.8 33.5 + - + +
806A ALA* 3.2 18.4 - - - +
808A LYS* 1.3 73.4 - - - +
810A LEU* 1.3 69.3 + - + +
812A VAL* 3.3 10.8 - - + +
813A LEU* 3.0 27.7 + - - +
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Residues in contact with LEU 810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A HIS* 6.0 0.7 - - - -
667A ARG* 3.4 43.4 + - - +
668A GLY* 4.7 1.3 - - - -
669A LEU* 4.3 5.3 - - + +
786A TYR* 3.6 36.8 - - + -
793A ILE* 6.1 2.0 - - + -
794A VAL* 3.6 37.5 - - + -
797A LEU* 6.0 0.2 - - + -
806A ALA 3.1 19.7 + - - +
807A ALA 3.8 1.1 - - - +
809A VAL* 1.3 86.3 - - + +
811A SER* 1.3 59.3 + - - +
813A LEU* 3.9 11.7 - - + -
814A GLY* 2.8 23.5 + - - -
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Residues in contact with SER 811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490A ILE 5.1 2.1 - - - +
491A GLU* 3.3 35.8 + - - +
492A THR* 3.2 14.6 + - - -
617A HIS* 6.0 0.9 - - - -
706A HIS* 5.4 2.7 - - - -
807A ALA 2.3 26.6 + - - -
808A LYS* 3.0 11.7 + - - -
810A LEU* 1.3 75.0 - - - +
812A VAL* 1.3 62.9 + - - +
814A GLY* 3.3 1.7 + - - -
815A ARG* 2.9 38.3 + - - +
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Residues in contact with VAL 812 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A CYS* 3.2 32.3 - - - +
700A ILE* 4.0 15.7 - - + -
706A HIS* 3.5 28.3 - - + -
735A VAL* 4.2 22.5 - - + +
739A VAL* 5.1 9.4 - - + -
808A LYS* 3.1 10.0 + - + +
809A VAL* 3.3 18.4 - - - +
811A SER* 1.3 74.0 - - - +
813A LEU* 1.3 61.0 + - - +
815A ARG* 3.6 5.3 - - - +
816A LEU* 2.9 27.4 + - - +
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Residues in contact with LEU 813 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669A LEU* 4.4 0.7 - - + -
732A ILE* 5.2 18.4 - - + -
735A VAL* 6.1 3.8 - - + -
781A LEU* 5.7 3.1 - - + -
786A TYR* 3.7 37.5 - - + +
809A VAL 3.0 21.5 + - - +
810A LEU* 3.9 15.3 - - + -
812A VAL* 1.3 76.9 - - + +
814A GLY* 1.3 66.2 + - - +
816A LEU* 3.1 24.2 + - + +
817A PHE* 3.5 44.1 - - + -
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Residues in contact with GLY 814 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A HIS* 6.6 0.2 - - - -
618A TYR* 5.6 2.3 - - - -
669A LEU* 3.7 25.4 - - - +
673A HIS* 3.0 31.4 + - - -
810A LEU 2.8 20.4 + - - -
811A SER* 3.3 2.9 + - - -
813A LEU* 1.3 77.9 - - - +
815A ARG* 1.3 58.0 + - - +
818A THR* 3.9 1.0 - - - +
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Residues in contact with ARG 815 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A ASN* 3.2 55.9 + - - +
490A ILE 4.5 6.5 - - - +
491A GLU* 5.8 4.1 - - - +
698A GLY 5.1 1.8 - - - +
699A CYS* 2.4 52.6 + - + +
700A ILE 3.7 2.0 + - - -
701A ARG* 4.2 17.1 - - - +
704A ASP* 5.0 3.2 + - - -
706A HIS* 3.0 39.6 + - - -
811A SER* 2.9 24.0 + - - +
812A VAL* 3.6 9.6 - - - +
814A GLY* 1.3 75.5 - - - +
816A LEU* 1.3 62.4 + - - +
818A THR* 3.2 16.9 - - + +
819A ASN* 3.2 12.3 + - - +
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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