Contacts of the helix formed by residues 768 - 781 (chain B) in PDB entry 1FO4
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 768 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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648B LEU* 5.7 0.6 - - - +
766B THR* 3.0 8.9 + - - +
767B GLN* 1.3 80.8 - - - +
769B ALA* 1.3 55.8 + - - +
770B MET* 3.6 8.8 + - - +
771B LYS* 3.1 43.3 + - + +
772B THR* 2.7 30.3 + - - -
802B GLU 3.0 28.9 + - - +
803B THR* 4.5 6.8 - - - +
806B THR* 5.7 1.1 - - + +
1074B SER 4.3 1.2 - - - +
1075B SER 4.8 0.2 - - - -
1076B PRO* 3.6 31.4 - - + +
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Residues in contact with ALA 769 (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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766B THR* 4.2 3.4 + - - +
767B GLN 4.0 1.8 + - - -
768B ASN* 1.3 71.7 - - - +
770B MET* 1.3 61.5 + - - +
772B THR* 3.4 2.6 + - - -
773B GLN* 2.9 31.4 + - - +
789B VAL* 3.9 23.8 - - + +
791B VAL* 4.4 12.1 - - + -
1036B THR* 5.4 2.7 - - + +
1066B THR* 5.1 12.6 - - + -
1067B SER* 5.6 0.4 - - - -
1068B THR* 3.8 22.1 - - + +
1074B SER* 4.9 8.0 + - - +
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Residues in contact with MET 770 (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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1025A THR* 3.6 37.5 - - + +
1121A TYR* 4.0 20.4 - - + +
768B ASN* 3.3 3.5 - - - +
769B ALA* 1.3 77.8 - - - +
771B LYS* 1.3 78.3 + - + +
773B GLN* 3.1 15.9 + - - +
774B SER* 2.9 32.7 + - - +
1068B THR* 4.4 3.3 - - - +
1073B ASN* 3.5 26.0 - - - +
1074B SER* 3.2 37.9 + - - +
1075B SER* 5.3 0.7 - - - -
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Residues in contact with LYS 771 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B LEU* 4.2 25.3 + - + +
768B ASN* 3.1 35.1 + - + +
770B MET* 1.3 95.6 - - + +
772B THR* 1.3 60.8 + - - +
774B SER* 3.5 7.8 + - - +
775B PHE* 2.9 67.8 + - + +
802B GLU 5.4 0.2 - - - +
803B THR* 5.8 2.9 - - + -
806B THR* 4.5 5.2 - - + -
1076B PRO* 6.1 0.2 - - + -
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Residues in contact with THR 772 (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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762B LEU* 4.8 1.6 - - + -
764B VAL* 4.3 12.6 - - + -
766B THR* 3.6 16.6 + - - +
768B ASN 2.7 23.8 + - - -
769B ALA 3.6 4.9 - - - -
771B LYS* 1.3 75.4 - - - +
773B GLN* 1.3 64.1 + - - +
775B PHE* 4.0 0.5 - - - +
776B VAL* 3.0 35.7 + - + +
789B VAL* 4.1 17.7 - - + -
805B SER* 4.5 1.0 + - - -
806B THR* 4.1 16.8 - - + +
809B SER* 3.7 33.0 + - - +
810B VAL* 6.4 0.2 - - - -
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Residues in contact with GLN 773 (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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1024A TYR* 3.5 37.5 + - - -
769B ALA 2.9 13.8 + - - +
770B MET* 3.3 15.3 - - - +
772B THR* 1.3 78.3 - - - +
774B SER* 1.3 58.6 + - - +
776B VAL* 3.4 2.4 + - - +
777B ALA* 3.0 28.1 + - - +
784B VAL* 3.3 28.3 + - + +
787B ILE* 2.8 39.5 + - + +
789B VAL* 3.8 14.1 - - + +
1068B THR* 3.5 21.1 + - + +
1073B ASN 5.4 1.6 + - - -
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Residues in contact with SER 774 (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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1025A THR* 5.6 5.8 - - - -
770B MET* 2.9 22.9 + - - +
771B LYS* 3.4 18.9 + - - +
773B GLN* 1.3 73.2 - - - +
775B PHE* 1.3 66.5 + - - +
777B ALA* 3.5 7.2 - - - +
778B LYS* 2.8 31.5 + - - +
784B VAL* 4.4 17.6 - - - +
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Residues in contact with PHE 775 (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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646B THR* 3.5 19.9 + - - +
647B GLY* 3.5 40.8 - - - -
648B LEU* 3.7 11.9 - - + -
771B LYS* 2.9 51.4 + - + +
772B THR 4.2 1.1 - - - +
774B SER* 1.3 78.3 - - - +
776B VAL* 1.3 61.6 + - - +
778B LYS* 3.4 15.0 + - + +
779B MET* 3.0 25.8 + - - +
803B THR* 5.3 5.4 - - + -
806B THR* 3.6 34.8 - - + -
810B VAL* 4.1 16.1 - - + +
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Residues in contact with VAL 776 (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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760B MET* 4.5 4.7 - - - -
762B LEU* 4.0 22.2 - - + -
772B THR* 3.0 32.5 + - + +
773B GLN 3.7 3.1 - - - +
775B PHE* 1.3 76.4 - - - +
777B ALA* 1.3 59.7 + - - +
779B MET* 3.5 5.0 + - - +
780B LEU* 3.0 43.6 + - + +
787B ILE* 4.0 20.2 - - + -
809B SER 4.2 6.5 - - - +
810B VAL* 4.4 13.0 - - + -
813B ALA* 3.8 26.5 - - + -
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Residues in contact with ALA 777 (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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773B GLN 3.0 17.9 + - - +
774B SER 3.2 4.7 + - - +
776B VAL* 1.3 75.6 - - - +
778B LYS* 1.3 54.8 + - - +
780B LEU 3.4 0.2 + - - -
781B GLY* 2.7 30.0 + - - -
782B VAL* 3.1 35.1 + - - +
784B VAL* 4.0 22.0 - - + -
787B ILE* 3.9 15.0 - - + -
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Residues in contact with LYS 778 (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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643B SER* 3.2 35.5 + - - -
645B GLU* 2.7 36.6 + - - +
646B THR* 5.1 4.3 - - - +
650B ASN* 3.0 28.3 - - - +
774B SER 2.8 20.0 + - - +
775B PHE* 3.7 16.2 - - + +
776B VAL 3.3 0.2 - - - -
777B ALA* 1.3 69.9 - - - +
779B MET* 1.3 65.6 + - - +
781B GLY* 3.2 11.6 + - - -
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Residues in contact with MET 779 (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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640B ILE* 3.2 19.6 - - + +
641B PRO* 4.2 0.9 - - - -
642B GLY* 2.8 24.9 + - - -
643B SER 3.4 11.9 - - - +
646B THR* 6.4 0.2 - - - -
654B VAL* 4.1 11.7 - - + -
775B PHE 3.0 16.8 + - - +
776B VAL 3.7 2.5 - - - +
778B LYS* 1.3 77.2 - - - +
780B LEU* 1.3 89.3 + - + +
810B VAL* 3.3 45.1 - - + +
813B ALA* 3.9 7.4 - - + -
814B LEU* 3.5 33.2 - - - +
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Residues in contact with LEU 780 (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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641B PRO* 3.6 20.1 - - + +
642B GLY* 3.9 4.5 + - - -
758B GLY 4.7 4.5 - - - +
760B MET* 3.9 19.5 - - + -
776B VAL* 3.0 36.3 + - + +
777B ALA 3.9 2.9 - - - +
779B MET* 1.3 101.7 - - + +
781B GLY* 1.3 63.8 + - - +
782B VAL* 3.9 19.5 - - + +
787B ILE* 3.9 16.2 - - + -
813B ALA 4.5 1.3 - - - +
817B TYR* 3.7 38.7 - - + -
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Residues in contact with GLY 781 (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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641B PRO 5.4 0.2 - - - -
642B GLY* 4.0 9.4 - - - -
777B ALA 2.7 9.8 + - - -
778B LYS* 3.2 11.8 + - - -
779B MET 3.3 0.4 + - - -
780B LEU* 1.3 81.0 - - - +
782B VAL* 1.3 60.1 + - - +
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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