Contacts of the helix formed by residues 804 - 821 (chain A) in PDB entry 4FWF
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 THR 804 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A ASN* 4.7 8.5 - - + +
795A GLU* 4.8 1.2 - - - +
801A PHE* 4.1 5.0 + - + +
802A PRO 3.0 14.7 + - - +
803A GLN* 1.3 81.5 - - + +
805A VAL* 1.3 58.7 + - - +
806A THR* 3.6 9.5 + - - -
807A GLY* 2.8 22.3 + - - -
808A ALA* 2.9 29.1 + - - +
904A FAD 3.3 22.0 + - + +
3E THR* 5.0 9.6 - - - +
4E MET* 4.2 19.1 - - + -
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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
----------------------------------------------------------
392A PRO* 4.0 18.6 - - + +
421A VAL* 3.9 10.5 - - + -
436A ALA* 3.4 28.9 - - + -
447A VAL* 4.6 5.4 - - + -
450A MET* 6.4 0.9 - - + -
579A TYR* 3.5 34.1 - - + -
582A ILE* 6.5 0.7 - - + -
583A ILE* 5.7 2.5 - - + -
804A THR* 1.3 70.3 - - - +
806A THR* 1.3 52.4 + - - +
808A ALA* 3.3 2.3 + - - +
809A TYR* 2.7 39.8 + - + +
904A FAD 2.8 37.5 + - + +
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Residues in contact with THR 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A VAL* 4.7 2.4 - - - +
445A ASN* 2.8 38.9 + - - +
446A PRO* 3.8 9.0 - - + -
447A VAL* 3.7 12.1 - - - +
568A PHE* 3.8 17.5 - - + -
579A TYR* 5.1 2.3 + - - -
801A PHE* 5.4 1.3 - - + -
804A THR* 3.2 9.4 - - - +
805A VAL* 1.3 77.8 - - - +
807A GLY* 1.3 57.7 + - - +
809A TYR* 3.6 5.8 - - - +
810A LEU* 2.9 50.2 + - + +
904A FAD 4.4 0.5 + - - -
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Residues in contact with GLY 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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795A GLU* 5.0 1.6 - - - -
798A ASN* 2.7 30.2 + - - -
801A PHE* 3.2 32.3 - - - +
802A PRO 5.4 0.2 - - - -
804A THR* 2.8 17.1 + - - -
806A THR* 1.3 73.8 - - - +
808A ALA* 1.3 55.9 + - - +
810A LEU* 4.6 0.2 - - - -
811A SER* 2.9 18.2 + - - -
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Residues in contact with ALA 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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392A PRO* 4.1 2.7 - - + -
393A ALA* 3.4 15.9 - - + +
795A GLU* 3.7 9.8 - - - +
804A THR 2.9 15.5 + - - +
805A VAL 3.7 5.4 - - - +
807A GLY* 1.3 69.0 - - - +
809A TYR* 1.3 66.3 + - - +
811A SER* 2.5 25.3 + - - -
812A GLY 2.9 5.9 + - - -
904A FAD 3.4 40.6 - - - +
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Residues in contact with TYR 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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364A THR* 4.1 4.9 - - - -
365A GLY* 3.3 29.3 + - - -
392A PRO* 4.1 10.8 - - + +
396A ALA* 3.3 39.6 - - + +
400A GLN* 4.6 2.9 + - - -
446A PRO* 3.6 33.2 - - + +
447A VAL* 5.9 0.7 - - + -
449A LEU* 5.7 0.2 - - - +
450A MET* 3.9 31.9 - - + -
586A LEU* 4.2 17.3 - - + -
805A VAL* 2.7 24.4 + - + +
806A THR* 3.6 5.4 - - - +
808A ALA* 1.3 70.7 - - - +
810A LEU* 1.3 65.5 + - + +
812A GLY* 2.9 18.4 + - - -
813A VAL* 3.0 35.2 + - + +
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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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282A LEU* 4.1 23.6 - - + -
446A PRO* 4.0 16.6 - - + -
568A PHE* 3.9 9.4 - - + -
798A ASN* 3.9 7.4 - - - +
801A PHE* 3.6 33.4 - - + -
806A THR* 2.9 40.5 + - + +
807A GLY 3.8 3.1 - - - +
809A TYR* 1.3 80.6 - - + +
811A SER* 1.3 52.9 + - - +
813A VAL* 3.2 12.1 + - + +
814A ARG* 2.7 36.0 + - - +
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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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793A ALA* 3.7 2.2 - - - +
794A GLY* 2.8 26.9 + - - -
797A THR* 3.5 23.8 - - - -
798A ASN* 3.9 5.0 - - - +
807A GLY 2.9 13.2 + - - -
808A ALA* 2.5 21.5 + - - -
810A LEU* 1.3 74.9 - - - +
812A GLY* 1.3 61.7 + - - +
814A ARG* 3.7 19.4 - - - +
815A GLU* 3.0 29.5 + - - +
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Residues in contact with GLY 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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393A ALA 3.4 25.6 - - - -
397A ALA* 3.5 17.5 - - - +
793A ALA* 4.2 5.6 - - - -
808A ALA 2.9 10.7 + - - -
809A TYR 2.9 5.1 + - - -
811A SER* 1.3 77.4 + - - +
813A VAL* 1.3 55.3 + - - +
815A GLU* 3.4 0.5 + - - -
816A ALA* 2.9 30.0 + - - +
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Residues in contact with VAL 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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358A ARG 4.7 1.0 - - - +
359A LYS 3.4 23.6 - - - +
360A GLY* 3.8 15.9 - - - +
364A THR* 5.0 2.7 - - + -
396A ALA* 4.3 1.8 - - + +
400A GLN* 4.0 22.6 + - + +
809A TYR* 3.0 46.0 + - + +
810A LEU* 3.6 15.5 - - + +
812A GLY* 1.3 71.3 - - - +
814A ARG* 1.3 66.8 + - - +
816A ALA* 3.5 6.9 + - - +
817A SER* 3.2 21.8 + - - -
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Residues in contact with ARG 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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359A LYS 5.8 0.2 - - - -
783A ALA* 3.7 12.3 - - - +
792A PHE 3.1 20.8 + - - -
797A THR* 2.8 43.8 + - - -
798A ASN* 4.3 7.9 - - - +
810A LEU 2.7 19.8 + - - +
811A SER* 3.7 23.1 - - - +
813A VAL* 1.3 77.5 - - - +
815A GLU* 1.3 81.2 + - - +
817A SER* 3.3 13.3 + - - -
818A LYS* 3.4 27.8 + - + +
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Residues in contact with GLU 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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624A LEU* 3.9 19.1 - - + -
783A ALA 3.6 3.4 - - - +
791A PHE* 3.4 19.9 - - - +
792A PHE 3.3 28.4 - - - +
793A ALA* 3.7 7.0 - - + -
811A SER 3.0 19.6 + - - +
812A GLY 4.0 2.7 - - - +
814A ARG* 1.3 100.6 + - - +
816A ALA* 1.3 66.0 + - - +
818A LYS* 2.8 35.6 + - - +
819A ILE* 2.8 30.8 + - + +
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Residues in contact with ALA 816 (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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397A ALA* 4.0 12.7 - - - +
400A GLN* 3.7 31.9 - - + +
401A LEU* 3.8 16.3 - - + +
404A PHE* 4.7 3.8 - - + -
812A GLY 2.9 18.2 + - - +
813A VAL 3.8 4.5 - - - +
815A GLU* 1.3 74.5 - - - +
817A SER* 1.3 58.1 + - - +
819A ILE* 3.4 5.9 + - - +
820A ALA* 2.9 32.2 + - - +
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Residues in contact with SER 817 (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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358A ARG* 2.9 62.4 + - - -
359A LYS* 3.6 27.3 - - - +
813A VAL 3.2 9.3 + - - -
814A ARG* 3.4 11.9 - - - -
815A GLU 3.1 0.8 - - - -
816A ALA* 1.3 79.0 - - - +
818A LYS* 1.3 61.9 + - - +
820A ALA* 3.3 3.1 + - - +
821A ALA 3.2 9.5 + - - -
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Residues in contact with LYS 818 (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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358A ARG* 4.9 0.9 - - - +
622A LYS* 5.7 0.5 - - - -
783A ALA* 3.7 15.4 + - - +
784A GLU* 5.1 1.4 - - - +
785A ASP* 4.2 20.9 + - - +
791A PHE* 4.1 14.0 - - + -
814A ARG* 3.7 25.7 - - + +
815A GLU* 2.8 43.6 + - - +
817A SER* 1.3 72.7 - - - +
819A ILE* 1.3 68.7 + - - +
821A ALA* 3.1 22.5 + - - +
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Residues in contact with ILE 819 (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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383A LYS* 3.1 26.4 + - + +
385A VAL* 3.7 33.2 - - + -
401A LEU* 4.2 21.3 - - + -
406A ILE* 5.2 0.9 - - + -
622A LYS* 3.7 21.1 - - + +
624A LEU* 4.3 24.0 - - + -
791A PHE* 3.8 38.4 - - + -
815A GLU 2.8 26.9 + - - +
816A ALA* 3.7 4.9 - - - +
818A LYS* 1.3 76.0 - - - +
820A ALA* 1.3 62.8 + - - +
821A ALA 3.3 0.3 + - - +
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Residues in contact with ALA 820 (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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358A ARG* 3.9 19.7 - - + -
376A LEU* 4.7 4.9 - - + -
380A TYR* 3.4 19.3 - - + +
383A LYS* 3.7 8.5 - - - -
404A PHE* 3.9 20.4 - - + -
406A ILE* 3.9 18.6 - - + -
816A ALA 2.9 18.1 + - - +
817A SER 3.8 4.0 - - - +
818A LYS 3.2 0.2 - - - -
819A ILE* 1.3 76.4 - - - +
821A ALA* 1.3 64.6 + - - +
822A PHE 4.3 0.7 - - - -
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Residues in contact with ALA 821 (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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358A ARG* 3.6 30.1 - - - +
380A TYR* 5.0 0.4 - - - -
383A LYS* 2.9 24.9 + - - -
817A SER 3.2 4.6 + - - +
818A LYS* 3.1 19.7 + - - +
819A ILE 3.9 0.9 - - - +
820A ALA* 1.3 75.9 - - - +
822A PHE* 1.3 64.3 + - + +
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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