Contacts of the helix formed by residues 789 - 802 (chain I) in PDB entry 5FUR
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 PHE 789 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335I ILE* 3.2 17.9 - - + -
336I ILE 3.7 0.2 - - - -
337I ASP* 1.0 204.8 - - + +
338I GLU* 2.3 18.6 - - + -
339I THR* 4.1 4.3 - - - -
788I LYS* 1.3 77.5 - - + +
790I SER* 1.3 65.5 + - - +
792I ASN* 2.7 26.7 + - - +
846I TYR* 5.2 5.3 + + - -
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Residues in contact with SER 790 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337I ASP* 2.9 9.4 - - - -
740I ASN* 3.1 41.4 + - - +
741I PHE* 4.2 2.4 - - - +
743I SER* 5.0 8.6 - - - -
747I TYR* 4.7 4.8 - - - -
788I LYS* 3.3 2.7 - - - +
789I PHE* 1.3 84.4 - - - +
791I ASP* 1.3 60.2 + - - +
792I ASN 2.9 7.1 + - - -
793I TYR* 3.0 28.9 + - - +
794I TYR 4.1 0.5 + - - -
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Residues in contact with ASP 791 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737I LYS* 5.8 0.2 - - - -
741I PHE* 2.8 44.5 - - + -
747I TYR* 4.7 0.9 - - - -
785I ARG* 6.0 0.4 - - - -
786I LYS 3.6 8.4 - - - +
787I ASN 3.5 1.6 - - - -
788I LYS* 2.4 57.1 + - + +
790I SER* 1.3 77.5 + - - +
792I ASN* 1.3 66.4 + - - +
794I TYR* 2.9 11.0 + - + +
795I ARG* 2.9 41.5 + - + +
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Residues in contact with ASN 792 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336I ILE 5.8 0.4 - - - -
337I ASP* 4.5 9.5 + - + +
788I LYS 3.4 8.7 + - - -
789I PHE* 2.7 28.5 + - - +
790I SER 2.9 1.0 + - - +
791I ASP* 1.3 81.4 + - - +
793I TYR* 1.3 61.4 + - + +
795I ARG* 2.8 32.1 + - - +
796I ALA* 2.8 34.1 + - - +
846I TYR* 3.3 30.9 - - - -
848I HIS* 3.6 34.1 + - + +
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Residues in contact with TYR 793 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337I ASP* 2.7 48.9 + - + -
338I GLU* 4.6 2.3 - - - -
339I THR* 4.7 7.0 + - - -
340I PRO* 5.3 4.2 - - + +
341I LEU* 3.4 32.3 - - + +
747I TYR* 3.9 17.5 - - + +
748I PHE* 5.2 22.0 - + + -
790I SER* 3.0 24.4 + - - +
792I ASN* 1.3 79.6 - - + +
794I TYR* 1.3 61.4 + - - +
796I ALA* 4.6 5.6 - - + -
797I GLU* 3.1 29.5 + - - +
848I HIS* 5.5 13.7 - + - -
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Residues in contact with TYR 794 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727I PHE* 5.3 8.1 - + - -
741I PHE* 3.8 22.0 - + - -
744I PHE* 5.2 3.9 - + - -
747I TYR* 2.8 56.8 - + + +
750I GLN* 3.9 22.8 + - + -
778I LEU* 3.7 19.9 - - + +
781I TYR* 5.1 2.3 - - - +
785I ARG* 3.0 48.3 + - - -
791I ASP* 2.9 11.5 + - - +
793I TYR* 1.3 77.9 - - - +
795I ARG* 1.3 63.1 + - + +
797I GLU 3.5 0.7 - - - -
798I MET* 2.8 44.9 + - + +
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Residues in contact with ARG 795 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741I PHE* 6.4 0.4 - - + -
785I ARG* 4.8 13.5 - - + +
786I LYS 4.5 10.8 + - - -
787I ASN* 3.5 27.5 + - - +
788I LYS 4.7 0.4 - - - +
791I ASP* 2.9 35.1 + - + +
792I ASN* 2.8 39.2 + - - +
794I TYR* 1.3 76.5 - - + +
796I ALA* 1.3 60.7 + - - +
798I MET* 3.1 28.9 - - + +
799I ILE* 2.9 32.6 + - - +
846I TYR* 4.3 5.7 - - - -
849I THR* 3.2 37.0 + - + +
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Residues in contact with ALA 796 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792I ASN 2.8 22.7 + - - +
793I TYR* 4.2 5.6 - - + +
795I ARG* 1.3 71.2 - - - +
797I GLU* 1.4 62.2 + - + +
799I ILE 3.2 14.4 + - - -
800I ASP* 3.6 11.2 + - - -
848I HIS* 4.4 19.3 - - + +
849I THR* 5.2 1.1 - - - +
852I VAL* 3.6 33.8 - - + +
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Residues in contact with GLU 797 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696I MET* 5.8 1.2 - - - +
747I TYR 3.2 19.9 - - - +
748I PHE* 3.4 35.4 - - - +
751I LYS* 2.9 52.0 - - + +
793I TYR* 3.1 19.2 + - - +
794I TYR 3.5 2.2 - - - -
796I ALA* 1.4 80.8 - - + +
798I MET* 1.3 55.7 + - - +
799I ILE 3.4 0.2 - - - -
800I ASP* 4.1 14.8 - - - +
801I ALA* 3.6 7.6 + - - +
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Residues in contact with MET 798 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751I LYS* 5.7 0.4 - - - +
778I LEU* 5.0 6.7 - - + -
782I ASN* 3.3 32.1 - - + +
783I ASP 5.8 0.2 - - - +
785I ARG* 3.3 29.6 - - - +
794I TYR* 2.8 31.0 + - + +
795I ARG* 3.1 41.3 - - + +
797I GLU* 1.3 75.4 - - - +
799I ILE* 1.3 72.5 + - + +
800I ASP 3.2 2.2 - - - -
801I ALA* 3.3 15.9 - - + +
802I LEU* 3.2 26.9 + - - +
849I THR* 6.1 1.3 - - + -
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Residues in contact with ILE 799 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795I ARG 2.9 23.0 + - - +
796I ALA 3.2 0.6 + - - -
798I MET* 1.3 93.0 - - + +
800I ASP* 1.3 55.0 + - - +
802I LEU* 3.2 4.2 + - + +
803I ALA* 2.8 35.1 + - - +
832I GLU* 5.4 3.1 - - + +
849I THR* 4.5 8.3 - - + +
852I VAL* 2.7 47.8 - - + +
853I SER* 4.0 14.4 - - - +
856I ARG* 3.0 47.2 - - + +
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Residues in contact with ASP 800 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751I LYS* 4.3 17.4 - - - -
755I VAL* 4.1 9.5 - - - +
758I ALA* 5.6 0.5 - - - +
796I ALA 3.6 9.9 + - - +
797I GLU* 4.2 19.0 - - - +
799I ILE* 1.3 79.2 - - - +
801I ALA* 1.4 57.8 + - - +
803I ALA* 2.9 27.2 - - - +
804I ASN* 4.8 4.5 + - - +
852I VAL* 4.9 12.3 - - - +
855I LEU* 5.2 6.2 - - - +
859I ARG* 4.4 16.5 + - - -
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Residues in contact with ALA 801 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751I LYS* 4.8 3.1 - - - +
754I PRO* 4.4 15.3 - - + +
755I VAL* 4.1 13.2 - - + -
758I ALA* 5.0 1.9 - - - +
775I ILE* 4.4 11.4 - - - +
778I LEU* 3.8 22.7 - - + -
797I GLU 3.6 5.4 + - - +
798I MET* 3.3 24.9 - - + +
799I ILE 3.2 0.2 - - - -
800I ASP* 1.4 81.6 - - - +
802I LEU* 1.3 57.0 - - - +
803I ALA 2.8 13.9 - - - +
804I ASN 4.2 1.6 - - - -
805I SER* 4.2 7.4 - - - -
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Residues in contact with LEU 802 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775I ILE* 4.1 11.9 - - + -
778I LEU* 4.4 14.6 - - + -
779I ILE* 3.2 34.5 - - + -
782I ASN* 3.8 18.6 - - - +
798I MET 3.2 17.2 + - - +
799I ILE* 3.2 8.4 + - + +
801I ALA* 1.3 73.2 - - - +
803I ALA* 1.3 62.3 + - - +
805I SER* 2.9 27.1 + - - -
806I VAL* 3.8 8.3 + - - +
829I ILE* 5.6 2.7 - - + +
832I GLU* 3.5 6.7 - - - +
856I ARG* 2.6 51.6 - - - +
860I VAL* 5.4 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
------------------------------------------------------------
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