Contacts of the helix formed by residues 692 - 705 (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 TYR 692 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339I THR* 5.7 1.3 - - + +
340I PRO* 6.2 4.7 - - + -
389I ASN* 2.9 38.1 + - + -
394I TRP* 4.1 21.0 - + + -
690I CYS 5.6 0.7 - - - -
691I PHE* 1.3 75.6 - - - +
693I ARG* 1.3 61.3 + - + +
695I ARG* 3.2 27.7 + - - +
696I MET* 3.0 24.8 + - - +
743I SER* 5.0 11.8 - - - -
746I SER* 3.5 30.4 + - - -
748I PHE* 3.9 32.1 - + + +
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Residues in contact with ARG 693 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340I PRO* 5.6 9.5 - - - +
341I LEU* 5.8 4.9 - - - +
394I TRP* 3.4 51.5 - - - +
397I GLU* 3.5 30.9 + - - -
663I GLN* 3.4 16.6 - - - +
691I PHE* 3.2 2.0 - - - +
692I TYR* 1.3 81.7 - - + +
694I VAL* 1.4 61.6 + - - +
696I MET* 3.3 28.7 - - + +
697I SER* 2.9 29.5 + - - -
748I PHE* 4.5 28.4 - - + -
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Residues in contact with VAL 694 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653I LEU* 5.7 1.8 - - + -
659I VAL* 3.9 13.2 - - + -
662I GLN* 4.0 20.9 - - + +
663I GLN* 3.4 35.6 + - + +
666I ILE* 5.4 2.2 - - + -
684I ILE* 4.3 11.4 - - + -
690I CYS* 3.2 34.5 - - + -
691I PHE* 3.2 16.0 - - + +
693I ARG* 1.4 73.9 - - - +
695I ARG* 1.3 62.8 + - - +
697I SER* 3.2 3.4 + - - +
698I ALA* 2.8 33.0 + - + +
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Residues in contact with ARG 695 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684I ILE 4.2 7.9 - - - +
685I LEU* 4.1 13.9 - - - +
686I GLU* 5.2 1.6 - - - +
687I GLN 4.4 11.4 + - - -
688I GLU* 5.3 6.8 - - - +
689I GLN 5.0 0.2 - - - -
690I CYS* 2.6 46.4 + - + +
691I PHE 2.9 18.3 + - - +
692I TYR* 3.2 35.7 + - - +
693I ARG 3.3 0.2 - - - -
694I VAL* 1.3 73.2 - - - +
696I MET* 1.3 69.6 + - - +
698I ALA* 3.0 15.7 + - - +
699I CYS 3.1 4.9 + - - -
745I GLN* 3.5 24.3 + - - +
746I SER* 3.2 17.6 + - - +
749I LEU* 2.8 35.9 - - + +
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Residues in contact with MET 696 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692I TYR 3.0 14.7 + - - +
693I ARG* 3.3 34.3 - - + +
695I ARG* 1.3 73.1 - - - +
697I SER* 1.3 60.3 + - - +
699I CYS* 2.7 31.0 + - - +
700I PHE* 3.0 9.4 + - + -
748I PHE* 3.3 38.6 - - + +
749I LEU* 3.3 12.0 - - - +
751I LYS* 5.9 0.2 - - - -
752I THR* 3.2 29.4 + - + +
797I GLU* 5.6 1.3 - - - +
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Residues in contact with SER 697 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663I GLN* 4.4 9.0 - - - +
666I ILE* 3.2 33.7 - - - +
667I LEU* 5.4 6.1 - - - -
670I GLU* 3.5 11.1 - - - +
693I ARG 2.9 22.4 + - - -
694I VAL* 3.5 8.7 + - - -
696I MET* 1.3 78.4 - - - +
698I ALA* 1.3 56.6 + - - +
700I PHE* 3.7 11.4 - - - -
701I CYS 3.1 19.4 + - - -
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Residues in contact with ALA 698 (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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653I LEU* 5.8 1.8 - - + -
666I ILE* 4.1 12.3 - - + +
681I LEU* 4.7 9.6 - - + +
684I ILE* 4.3 25.1 - - + -
685I LEU* 3.8 17.5 - - + +
694I VAL* 2.8 17.6 + - + +
695I ARG 3.3 6.3 - - - +
696I MET 2.9 0.2 + - - -
697I SER* 1.3 74.8 - - - +
699I CYS* 1.3 64.9 + - - +
701I CYS* 3.0 20.1 + - - +
702I LEU* 3.7 3.1 + - - +
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Residues in contact with CYS 699 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685I LEU* 3.6 10.8 - - + +
695I ARG 3.1 4.2 + - - -
696I MET 2.7 17.7 + - - +
698I ALA* 1.3 69.2 - - - +
700I PHE* 1.3 55.1 + - - +
702I LEU* 2.9 16.1 + - - +
703I ALA* 2.9 21.8 + - - +
749I LEU* 3.7 16.4 - - + -
752I THR* 2.6 38.1 - - - +
753I MET* 3.1 36.1 - - - -
756I ALA* 3.7 5.6 - - - +
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Residues in contact with PHE 700 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667I LEU* 5.6 2.0 - - + -
670I GLU* 2.8 46.9 - - - +
696I MET* 3.0 7.8 + - + +
697I SER* 3.5 15.0 + - - -
698I ALA 3.3 0.4 - - - -
699I CYS* 1.3 73.0 - - - +
701I CYS* 1.3 59.9 + - - +
703I ALA* 3.6 12.1 - - + -
704I LYS* 2.9 31.1 + - + -
751I LYS* 5.7 2.5 - - - -
752I THR* 4.8 19.0 + - + -
755I VAL* 5.3 10.8 - - + -
759I LEU* 4.2 24.9 - - + -
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Residues in contact with CYS 701 (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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666I ILE* 3.1 38.4 - - + -
669I LEU* 3.6 16.4 - - - -
670I GLU* 3.5 9.8 - - - +
677I SER* 4.8 0.4 - - - -
681I LEU* 3.8 13.7 - - + -
697I SER 3.1 5.1 + - - -
698I ALA 3.0 10.8 + - - +
700I PHE* 1.3 74.1 - - - +
702I LEU* 1.3 66.5 + - - +
704I LYS* 3.1 1.4 + - - +
705I ILE* 2.9 54.9 + - - +
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Residues in contact with LEU 702 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678I ARG* 3.3 44.6 - - + +
698I ALA 3.7 2.6 + - - +
699I CYS* 2.9 11.5 + - - +
701I CYS* 1.3 80.2 - - - +
703I ALA* 1.3 62.9 + - - +
705I ILE* 4.7 6.1 - - + +
706I ALA* 3.2 20.9 + - - +
707I ASN* 6.2 1.8 - - - +
715I GLY* 4.5 15.9 - - - +
718I ALA* 4.9 9.6 - - + -
719I MET* 3.4 43.1 - - + +
753I MET* 5.7 2.9 - - + -
756I ALA* 5.1 0.9 - - + -
760I LEU* 5.8 0.2 - - - +
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Residues in contact with ALA 703 (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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699I CYS 2.9 6.5 + - - -
700I PHE* 3.5 25.6 - - + +
701I CYS 3.0 0.2 - - - -
702I LEU* 1.3 80.1 - - - +
704I LYS* 1.3 63.6 + - - +
706I ALA* 3.3 14.9 - - - +
752I THR 5.0 0.2 - - - +
755I VAL 4.2 0.2 - - - +
756I ALA* 3.2 40.4 - - + +
759I LEU* 3.4 26.8 - - + +
760I LEU* 4.5 1.8 + - - +
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Residues in contact with LYS 704 (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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670I GLU* 2.9 43.3 - - + +
671I LYS* 4.9 15.7 - - + +
700I PHE* 2.9 25.6 + - + +
701I CYS 3.9 0.9 - - - +
703I ALA* 1.3 79.2 - - - +
705I ILE* 1.3 64.5 + - - +
706I ALA* 3.5 6.2 - - - +
759I LEU* 3.7 17.5 - - + +
763I VAL* 5.6 2.1 - - - +
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Residues in contact with ILE 705 (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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669I LEU 3.4 25.8 - - - +
670I GLU 4.1 7.2 - - - +
672I PHE 5.6 0.9 - - - +
674I THR* 3.5 22.2 - - - +
675I PRO 5.8 0.7 - - - +
677I SER* 5.0 6.1 - - - +
678I ARG* 5.7 15.0 - - + -
701I CYS* 2.9 34.1 + - - +
702I LEU* 4.4 5.6 - - + +
704I LYS* 1.3 76.5 - - - +
706I ALA* 1.3 66.7 + - - +
707I ASN 3.0 9.4 + - - +
708I SER* 3.6 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