Contacts of the helix formed by residues 661 - 676 (chain G) 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 LEU 661 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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659G PRO* 3.7 3.0 - - - +
660G LEU* 1.3 76.9 - - - +
662G LYS* 1.3 65.6 + - + +
664G ILE* 3.2 14.4 + - + +
665G LYS* 3.1 58.7 + - + +
32H VAL* 4.3 8.3 + - + +
33H GLN* 3.5 26.7 - - - +
34H SER 4.0 4.3 - - - +
35H GLY* 3.8 26.9 - - - +
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Residues in contact with LYS 662 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660G LEU 3.4 0.6 - - - -
661G LEU* 1.3 79.4 - - + +
663G HIS* 1.3 58.2 + - - +
665G LYS* 3.9 7.6 - - + +
666G LYS* 3.0 30.0 + - - +
35H GLY* 4.1 23.5 + - - +
36H HIS* 5.5 3.5 - - - +
37H VAL* 4.7 19.5 - - + +
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Residues in contact with HIS 663 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659G PRO 5.6 0.4 - - - +
660G LEU* 3.0 23.1 + - + +
662G LYS* 1.3 76.9 - - - +
664G ILE* 1.3 64.2 + - - +
666G LYS* 3.4 7.8 + - - +
667G LYS* 3.0 38.5 + - + +
693G THR* 5.4 0.4 - - - +
695G LYS* 3.3 39.6 + - + +
696G ASP* 3.0 25.7 + - + +
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Residues in contact with ILE 664 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660G LEU* 2.7 36.4 + - + +
661G LEU* 3.7 13.7 - - + +
663G HIS* 1.3 75.3 - - - +
665G LYS* 1.3 64.4 + - + +
667G LYS* 4.0 1.7 - - - +
668G ALA* 3.1 24.4 + - + +
695G LYS 3.4 17.7 - - - +
696G ASP* 4.2 7.1 - - - +
697G GLY* 4.6 12.0 + - - +
698G ASP* 5.8 3.4 - - - +
795G ARG* 3.4 44.4 - - + +
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Residues in contact with LYS 665 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661G LEU* 3.1 56.0 + - + +
662G LYS* 3.9 6.3 - - + +
664G ILE* 1.3 79.8 - - + +
666G LYS* 1.3 57.9 + - - +
668G ALA* 3.3 6.1 + - - +
669G LYS* 2.9 33.9 + - + +
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Residues in contact with LYS 666 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662G LYS 3.0 20.2 + - - +
663G HIS* 3.8 8.5 - - - +
664G ILE 3.3 0.2 - - - -
665G LYS* 1.3 77.2 - - - +
667G LYS* 1.3 60.0 + - + +
669G LYS* 3.2 13.5 + - + +
670G MET* 2.8 37.2 + - + +
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Residues in contact with LYS 667 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663G HIS* 3.0 30.4 + - + +
664G ILE 4.0 0.7 - - - +
666G LYS* 1.3 74.6 - - + +
668G ALA* 1.3 66.5 + - - +
670G MET* 3.8 33.8 - - - +
671G ARG* 2.9 66.6 + - - +
690G GLN* 5.5 4.0 + - - +
691G ASP* 3.7 13.9 + - - +
696G ASP* 3.5 34.4 + - + +
697G GLY 5.4 0.2 - - - +
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Residues in contact with ALA 668 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664G ILE* 3.1 19.6 + - + +
665G LYS* 3.6 7.0 - - - +
667G LYS* 1.3 75.6 - - - +
669G LYS* 1.3 62.8 + - - +
671G ARG* 3.4 7.5 + - - +
672G GLU* 3.0 24.3 + - - +
697G GLY* 5.9 3.9 - - - +
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Residues in contact with LYS 669 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665G LYS* 2.9 19.6 + - + +
666G LYS* 3.4 16.6 - - + +
668G ALA* 1.3 73.2 - - - +
670G MET* 1.3 66.5 + - - +
672G GLU* 3.2 7.5 + - + +
673G GLN* 3.0 52.9 + - + +
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Residues in contact with MET 670 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666G LYS* 2.8 27.7 + - + +
667G LYS* 3.8 39.9 - - - +
669G LYS* 1.3 71.5 - - - +
671G ARG* 1.3 78.5 + - + +
673G GLN* 3.2 11.3 + - - +
674G GLU* 3.0 44.4 + - + +
685G PHE* 5.7 0.7 - - + -
687G ARG* 5.8 3.1 - - - +
691G ASP* 5.6 1.3 - - - +
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Residues in contact with ARG 671 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667G LYS* 2.9 42.6 + - + +
668G ALA* 3.7 7.5 - - - +
670G MET* 1.3 87.9 - - + +
672G GLU* 1.3 58.3 + - - +
674G GLU* 3.3 3.5 + - - -
675G ARG 3.0 22.2 + - - -
685G PHE* 3.3 58.3 + - + +
686G MET* 4.0 10.1 - - - +
691G ASP* 3.5 36.6 + - - +
696G ASP* 2.9 32.1 + - - -
697G GLY* 4.2 8.9 - - - +
78H LYS* 4.0 1.4 - - - +
80H ILE* 4.0 27.0 - - + +
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Residues in contact with GLU 672 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668G ALA 3.0 16.8 + - - +
669G LYS* 3.7 7.4 - - + +
671G ARG* 1.3 75.8 - - - +
673G GLN* 1.3 60.1 + - + +
675G ARG* 3.1 35.3 + - - +
676G GLN* 3.0 51.2 + - + +
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Residues in contact with GLN 673 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669G LYS* 3.0 46.5 + - + +
670G MET* 3.2 10.5 + - - +
672G GLU* 1.3 76.2 - - + +
674G GLU* 1.3 60.8 + - - +
676G GLN* 3.2 7.0 + - - +
677G ALA* 2.8 31.1 + - - +
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Residues in contact with GLU 674 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670G MET* 3.0 36.9 + - + +
671G ARG 3.6 8.3 - - - +
673G GLN* 1.3 76.6 - - - +
675G ARG* 1.3 62.6 + - - +
677G ALA* 3.4 15.0 + - + +
678G SER* 3.7 10.0 + - - -
683G MET* 3.6 18.6 - - + +
685G PHE* 4.2 6.4 - - + -
687G ARG* 2.9 38.0 + - - -
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Residues in contact with ARG 675 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671G ARG 3.0 13.2 + - - +
672G GLU* 3.1 37.1 + - - +
674G GLU* 1.3 79.1 - - - +
676G GLN* 1.3 75.8 + - - +
680G GLY* 3.0 13.1 + - - +
681G GLY 3.0 34.6 + - - +
682G GLU* 5.7 0.2 - - - -
683G MET* 3.8 29.9 + - + +
685G PHE* 3.8 20.4 - - + -
80H ILE* 4.2 14.3 - - - +
81H ASP* 6.3 1.0 - - - +
475I LYS* 2.9 21.8 + - - -
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Residues in contact with GLN 676 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672G GLU* 3.0 44.3 + - + +
673G GLN* 3.2 6.5 + - - +
675G ARG* 1.3 89.2 - - - +
677G ALA* 1.3 57.1 + - - +
678G SER 3.2 3.1 - - - -
679G GLY* 3.2 30.5 - - - +
680G GLY* 4.3 5.9 - - - -
479I LEU* 4.3 5.7 - - - +
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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