Contacts of the helix formed by residues 772 - 787 (chain B) in PDB entry 4PE5
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 TRP 772 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B ASP 3.1 28.0 - - - -
404B ASP* 4.4 7.4 - - - -
406B LEU* 3.8 27.0 - - + +
472B VAL* 3.6 35.7 - - + -
473B LYS 4.9 1.1 - - - -
474B PHE* 3.9 29.8 - + + -
507B TYR* 3.2 42.2 + + + -
508B MET* 5.3 4.0 - - - -
766B ILE* 4.3 7.0 - - + -
770B SER* 3.2 9.3 + - - +
771B GLY* 1.3 83.5 - - - +
773B LYS* 1.3 60.6 + - - +
774B ARG 3.3 2.0 - - - -
775B GLN* 3.3 6.1 + - + +
776B VAL* 2.8 42.6 + - + +
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Residues in contact with LYS 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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524B ASP* 5.2 10.5 - - + +
525B PHE 5.6 5.4 - - - +
526B SER* 5.6 2.0 - - - +
766B ILE* 3.6 25.5 - - + +
770B SER* 5.4 6.3 - - - +
771B GLY 3.5 0.6 - - - -
772B TRP* 1.3 78.2 - - - +
774B ARG* 1.3 57.3 + - - +
776B VAL* 3.9 4.3 - - - +
777B ASP* 2.9 43.1 + - - +
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Residues in contact with ARG 774 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771B GLY 4.6 5.5 + - - +
772B TRP 3.3 0.4 - - - -
773B LYS* 1.3 80.6 - - - +
775B GLN* 1.3 58.9 + - - +
777B ASP* 3.2 7.2 + - - +
778B LEU* 2.9 57.2 + - + +
188C GLU* 3.6 49.7 + - + +
524C ALA 3.8 11.3 + - - -
525C GLN* 3.0 38.6 + - - +
526C TYR* 5.0 0.8 - - - +
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Residues in contact with GLN 775 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B SER* 5.4 4.2 + - - -
472B VAL* 3.6 36.3 - - + +
771B GLY 4.8 3.5 + - - +
772B TRP* 3.3 12.5 + - + +
774B ARG* 1.3 79.4 - - - +
776B VAL* 1.3 58.0 + - - +
778B LEU* 3.7 21.5 - - - +
779B ALA* 2.9 28.1 + - - +
188C GLU* 3.8 18.0 - - - +
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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
----------------------------------------------------------
468B ILE* 4.9 8.3 - - + -
472B VAL* 4.4 14.6 - - + -
474B PHE* 5.6 2.2 - - + -
508B MET* 3.8 25.6 - - + -
526B SER* 3.8 26.5 - - - +
764B ILE* 4.5 11.4 - - + -
766B ILE* 5.4 3.6 - - + -
772B TRP* 2.8 31.0 + - + +
773B LYS* 3.9 4.3 - - - +
775B GLN* 1.3 73.5 - - - +
777B ASP* 1.3 60.9 + - - +
779B ALA* 3.1 6.4 + - - +
780B ILE* 2.9 38.4 + - + +
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Residues in contact with ASP 777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B PHE 4.9 2.8 - - - +
526B SER* 3.3 11.4 - - - -
527B VAL* 2.7 43.7 + - + +
773B LYS* 2.9 32.0 + - - +
774B ARG* 3.5 7.2 - - - +
776B VAL* 1.3 76.4 - - - +
778B LEU* 1.3 59.4 + - + +
780B ILE 3.3 0.2 + - - -
781B LEU* 2.9 41.7 + - + +
524C ALA* 6.1 0.9 - - + -
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Residues in contact with LEU 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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774B ARG* 2.9 45.0 + - + +
775B GLN* 3.7 26.2 - - - +
777B ASP* 1.3 77.8 - - + +
779B ALA* 1.3 58.1 + - - +
781B LEU* 4.5 1.8 - - - -
782B GLN* 2.9 26.3 + - - +
521C ASN* 3.0 27.1 + - - +
524C ALA* 3.6 34.8 - - + +
525C GLN* 3.7 26.9 - - + +
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Residues in contact with ALA 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B ILE* 4.1 15.5 - - + -
471B SER* 3.9 22.4 - - - +
472B VAL* 4.0 14.8 - - + -
775B GLN 2.9 18.2 + - - +
776B VAL* 3.1 6.3 + - - +
778B LEU* 1.3 74.1 - - - +
780B ILE* 1.3 59.3 + - - +
782B GLN* 3.1 7.6 + - - +
783B LEU* 2.9 34.8 + - + +
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Residues in contact with ILE 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B ILE* 5.2 3.8 - - + -
468B ILE* 4.3 13.5 - - + -
526B SER* 3.6 24.9 - - - +
527B VAL* 3.5 32.1 - - + +
529B PHE* 3.8 34.3 - - + -
764B ILE* 4.3 11.9 - - + -
776B VAL* 2.9 26.1 + - + +
779B ALA* 1.3 73.8 - - - +
781B LEU* 1.3 59.2 + - - +
783B LEU* 3.0 13.4 + - - +
784B PHE* 2.9 32.5 + - + -
789B MET* 4.4 6.3 - - + -
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Residues in contact with LEU 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B VAL* 3.6 30.5 - - + -
777B ASP* 2.9 26.7 + - + +
778B LEU 4.0 1.3 - - - +
780B ILE* 1.3 75.5 - - - +
782B GLN* 1.3 56.7 + - - +
784B PHE* 3.2 18.3 + - + +
785B GLY* 2.9 23.7 + - - -
519C ILE* 3.6 35.9 - - + +
520C ASN* 3.3 21.5 - - - +
521C ASN* 3.6 25.3 + - + +
524C ALA* 3.7 17.5 - - + -
529C PHE* 5.4 0.2 - - + -
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Residues in contact with GLN 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B SER* 5.7 2.5 - - - +
778B LEU 2.9 20.6 + - - +
779B ALA* 3.2 10.3 - - - +
781B LEU* 1.3 75.6 - - - +
783B LEU* 1.3 60.7 + - + +
785B GLY* 3.8 1.3 - - - +
786B ASP* 2.9 31.9 + - - +
521C ASN* 3.4 22.2 - - - +
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Residues in contact with LEU 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B ILE* 4.0 18.2 - - + -
467B LYS* 4.0 31.0 - - + +
468B ILE* 4.6 13.9 - - + -
471B SER* 5.6 4.3 - - - -
779B ALA* 2.9 24.7 + - + +
780B ILE* 3.0 13.9 + - - +
782B GLN* 1.3 77.9 - - + +
784B PHE* 1.3 63.3 + - - +
786B ASP* 4.1 4.0 - - - +
787B GLY 3.2 15.4 + - - -
788B GLU* 3.4 21.8 + - + -
789B MET* 3.5 29.9 + - + +
792B LEU* 5.1 4.3 - - + -
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Residues in contact with PHE 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B VAL* 4.5 4.7 - - + -
528B PRO 3.2 27.4 - - - -
529B PHE* 3.6 13.9 - - - -
780B ILE* 2.9 13.6 + - + -
781B LEU* 3.2 35.6 + - + +
783B LEU* 1.3 77.2 - - - +
785B GLY* 1.3 62.6 + - - +
787B GLY* 3.2 13.5 + - - -
789B MET* 3.5 44.6 - - + +
519C ILE 4.7 1.8 - - - +
520C ASN* 6.0 0.7 - - - -
692C TYR* 4.3 0.3 - - - -
754C PHE* 3.6 29.4 - - + -
755C ARG* 3.8 29.4 - - + -
756C SER* 4.4 16.4 - - - -
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Residues in contact with GLY 785 (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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781B LEU 2.9 15.3 + - - -
782B GLN* 3.9 2.2 - - - -
783B LEU 3.4 0.2 - - - -
784B PHE* 1.3 76.5 - - - +
786B ASP* 1.3 61.3 + - - +
787B GLY 3.4 0.5 + - - -
520C ASN* 6.3 1.3 - - - -
521C ASN* 5.9 1.3 - - - -
522C GLU* 5.7 7.2 - - - -
692C TYR* 3.5 22.1 - - - +
695C ARG 5.0 5.3 - - - +
696C GLN* 3.7 7.1 - - - +
754C PHE* 3.9 14.0 - - - -
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Residues in contact with ASP 786 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782B GLN 2.9 19.0 + - - +
783B LEU* 4.1 6.3 - - + +
785B GLY* 1.3 75.7 - - - +
787B GLY* 1.3 60.8 + - - +
788B GLU* 3.3 10.7 + - + +
695C ARG 5.8 1.6 - - - -
696C GLN* 3.0 27.4 + - - +
698C GLU* 4.5 1.6 - - - +
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Residues in contact with GLY 787 (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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783B LEU 3.2 5.6 + - - -
784B PHE* 3.2 9.6 + - - -
785B GLY 3.2 4.3 - - - -
786B ASP* 1.3 78.5 - - - +
788B GLU* 1.3 62.4 + - - +
789B MET* 3.1 3.6 - - - -
790B GLU* 3.3 28.7 + - - +
791B GLU* 3.6 11.5 + - - +
692C TYR* 4.8 12.1 - - - -
696C GLN* 5.0 0.7 - - - -
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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
------------------------------------------------------------
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