Contacts of the helix formed by residues 659 - 671 (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 VAL 659 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393I HIS* 3.0 35.4 + - + +
657I ARG 4.9 2.7 - - - +
658I ASP* 1.3 71.8 + - - +
660I VAL* 1.3 65.7 + - - +
662I GLN* 2.8 41.8 + - - +
663I GLN* 3.1 23.9 + - + +
689I GLN 6.0 0.2 - - - +
690I CYS* 4.7 13.9 - - + -
691I PHE* 3.1 27.6 - - + -
694I VAL* 3.9 8.1 - - + -
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Residues in contact with VAL 660 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392I ARG* 4.0 19.3 - - + +
393I HIS* 4.3 7.9 - - - +
396I LYS* 3.0 66.5 - - + +
633I ASP* 3.6 14.4 - - - +
634I MET* 4.1 3.9 - - + +
658I ASP* 2.7 26.8 + - - +
659I VAL* 1.3 70.6 - - - +
661I ALA* 1.3 64.1 + - - +
663I GLN* 3.9 8.0 + - - +
664I GLU* 3.7 19.6 + - - +
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Residues in contact with ALA 661 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631I ASP 5.1 1.6 - - - +
632I PRO* 4.3 5.4 - - + -
633I ASP* 3.3 30.7 - - - +
634I MET 4.7 2.0 - - - +
652I GLN* 5.0 2.7 - - + -
656I GLU* 4.3 21.1 - - + -
658I ASP 3.1 13.3 + - - +
660I VAL* 1.3 81.4 - - - +
662I GLN* 1.3 59.9 + - - +
664I GLU* 3.0 7.3 + - - +
665I SER* 2.8 34.3 + - - +
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Residues in contact with GLN 662 (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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652I GLN 3.2 20.4 + - - +
653I LEU* 3.3 30.6 + - + +
654I ARG 4.9 2.0 + - - -
656I GLU* 3.0 28.4 + - + +
659I VAL* 2.8 43.5 + - + +
661I ALA* 1.3 77.7 - - - +
663I GLN* 1.3 56.8 + - - +
665I SER* 3.6 8.4 - - - -
666I ILE* 2.9 31.4 + - - +
684I ILE* 4.4 9.7 - - - +
690I CYS* 4.1 10.9 - - - -
694I VAL* 4.0 14.4 - - + +
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Residues in contact with GLN 663 (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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393I HIS 2.9 28.1 + - - -
394I TRP* 4.7 2.0 - - - +
396I LYS* 6.3 0.2 - - - +
659I VAL* 3.1 13.3 + - + +
660I VAL* 4.6 5.4 - - - +
662I GLN* 1.3 76.8 - - - +
664I GLU* 1.3 61.3 + - + +
666I ILE* 3.1 12.7 - - - +
667I LEU* 3.0 32.2 + - + +
691I PHE* 3.3 13.9 - - - +
693I ARG* 3.4 31.0 - - - +
694I VAL* 3.4 32.3 + - + -
697I SER* 4.4 5.8 + - - +
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Residues in contact with GLU 664 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396I LYS* 6.1 0.4 - - + -
400I ASP* 3.3 25.2 - - - +
634I MET* 3.2 46.3 - - + +
649I TRP* 4.4 3.0 - - - -
660I VAL* 3.7 9.1 + - + +
661I ALA* 3.0 9.2 + - - +
663I GLN* 1.3 81.1 - - + +
665I SER* 1.3 58.3 + - - +
667I LEU* 3.3 31.7 + - - +
668I ALA* 3.1 26.5 + - - +
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Residues in contact with SER 665 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649I TRP* 3.5 19.2 - - - -
652I GLN* 2.4 41.8 + - - +
653I LEU* 3.4 21.8 - - - -
661I ALA* 2.8 18.7 + - - +
662I GLN 3.0 2.9 + - - -
664I GLU* 1.3 78.0 - - - +
666I ILE* 1.3 58.4 + - - +
668I ALA 3.8 1.1 - - - -
669I LEU* 3.0 28.9 + - - +
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Residues in contact with ILE 666 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653I LEU* 3.9 11.6 - - + +
662I GLN 2.9 14.0 + - - +
663I GLN* 3.1 18.2 - - - +
665I SER* 1.3 76.7 - - - +
667I LEU* 1.3 60.0 + - - +
668I ALA 3.2 0.4 - - - -
669I LEU* 3.1 28.5 - - + -
670I GLU* 2.9 33.8 + - - +
681I LEU* 3.5 8.7 - - + -
694I VAL* 5.2 3.1 - - + +
697I SER* 3.2 47.6 - - - +
698I ALA* 4.1 6.1 - - - -
701I CYS* 3.1 30.7 - - + -
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Residues in contact with LEU 667 (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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663I GLN 3.0 18.5 + - - +
664I GLU* 3.3 43.5 + - - +
666I ILE* 1.3 74.6 - - + +
668I ALA* 1.3 57.0 + - - +
670I GLU* 3.2 27.2 - - - +
671I LYS* 3.1 39.9 + - + +
697I SER* 5.4 6.3 - - - -
700I PHE* 5.6 1.6 - - + -
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Residues in contact with ALA 668 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649I TRP* 2.9 55.0 - - + -
664I GLU 3.1 9.5 + - - +
667I LEU* 1.3 74.3 - - - +
669I LEU* 1.3 60.4 + - - +
670I GLU 3.2 0.7 - - - -
671I LYS* 3.0 1.6 + - - +
672I PHE* 2.8 48.4 + - + +
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Residues in contact with LEU 669 (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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646I ASP* 4.2 9.6 - - - +
649I TRP* 3.1 26.9 - - + -
650I GLN* 4.6 1.8 - - + +
653I LEU* 3.3 25.1 - - + -
665I SER 3.0 18.5 + - - +
666I ILE* 3.1 33.9 - - + -
667I LEU 3.5 0.2 - - - -
668I ALA* 1.3 78.2 - - - +
670I GLU* 1.4 62.4 + - - +
672I PHE 3.6 3.6 - - - +
674I THR* 3.6 31.1 + - + -
677I SER* 4.5 11.0 - - - +
681I LEU* 3.2 18.6 - - + -
701I CYS* 3.6 5.4 - - - -
705I ILE* 3.4 18.5 - - - +
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Residues in contact with GLU 670 (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 2.9 22.5 + - - +
667I LEU* 3.2 25.7 - - - +
668I ALA 3.2 0.2 - - - -
669I LEU* 1.4 80.8 - - - +
671I LYS* 1.3 68.3 + - + +
672I PHE 4.6 0.2 - - - +
697I SER* 3.5 15.9 - - - +
700I PHE* 2.8 66.9 - - - +
701I CYS* 3.5 12.1 - - - +
704I LYS* 2.9 32.6 - - + +
705I ILE* 4.1 8.7 - - - +
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Residues in contact with LYS 671 (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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667I LEU* 3.1 21.9 + - - +
668I ALA* 3.0 2.9 + - - +
670I GLU* 1.3 90.7 - - + +
672I PHE* 1.3 77.8 + - + +
673I PRO* 3.6 3.6 - - - +
704I LYS* 4.7 15.7 - - - +
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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
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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