Contacts of the helix formed by residues 669 - 688 (chain G) in PDB entry 5JLH
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 THR 669 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555G ASP* 2.7 28.4 + - - -
558G CYS* 4.1 6.3 - - - -
559G TRP* 3.6 29.5 - - + +
614G ASN* 3.4 27.1 - - - +
615G MET* 5.4 1.3 - - - -
616G ASP* 4.5 0.4 - - - +
667G PHE 3.5 13.2 - - - +
668G ARG* 1.3 74.7 - - - +
670G VAL* 1.3 66.4 + - - +
672G GLN* 2.9 27.6 + - - +
673G LEU* 2.9 18.5 + - - +
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Residues in contact with VAL 670 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288G LYS* 4.6 8.1 - - + +
289G SER* 5.3 6.7 - - - -
445G LYS* 3.3 33.7 - - - +
490G PHE* 3.3 28.0 - - + -
613G LYS 3.4 14.6 - - - +
614G ASN* 3.0 21.0 + - - +
616G ASP* 3.7 13.4 - - + +
669G THR* 1.3 72.0 - - - +
671G GLY* 1.3 70.3 + - - +
673G LEU* 3.8 10.3 - - - +
674G TYR* 2.9 33.0 + - - +
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Residues in contact with GLY 671 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490G PHE* 4.3 4.0 - - - -
494G CYS* 5.4 1.6 - - - -
551G LEU* 4.3 31.9 - - - +
555G ASP* 4.8 3.1 - - - -
614G ASN* 3.2 10.9 + - - -
669G THR* 4.3 0.2 - - - -
670G VAL* 1.3 87.1 - - - +
672G GLN* 1.3 60.7 + - - +
674G TYR* 3.6 6.1 - - - +
675G LYS* 3.0 23.7 + - - +
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Residues in contact with GLN 672 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D GLU* 4.5 14.6 + - - +
3D GLU* 4.9 11.2 + - - +
552G ALA* 6.0 1.2 - - - -
555G ASP* 3.7 12.9 + - - +
663G ARG* 3.8 28.8 + - - +
668G ARG* 5.5 1.8 - - - -
669G THR* 2.9 29.0 + - - +
671G GLY* 1.3 77.3 - - - +
673G LEU* 1.3 58.0 + - + +
675G LYS* 3.2 19.1 + - - +
676G GLU* 2.9 34.3 + - - +
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Residues in contact with LEU 673 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288G LYS* 3.4 22.4 - - - +
449G GLU* 5.5 2.7 - - - +
616G ASP* 3.2 27.8 - - - +
664G ARG* 5.5 5.2 - - - -
668G ARG* 3.3 37.0 - - + +
669G THR 2.9 18.7 + - - +
670G VAL* 3.8 6.7 - - - +
672G GLN* 1.3 77.6 - - + +
674G TYR* 1.3 56.7 + - - +
676G GLU* 3.1 14.9 + - - +
677G SER* 2.9 30.1 + - - -
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Residues in contact with TYR 674 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285G LEU* 2.9 43.3 - - + +
286G LEU 4.3 16.8 - - - -
287G GLU* 5.4 5.4 - - + -
494G CYS* 3.0 58.8 + - + -
495G ILE* 3.8 10.6 + - + +
497G TYR* 4.6 14.1 - + - -
498G THR* 3.2 9.4 - - - +
551G LEU* 5.7 3.6 - - + -
670G VAL 2.9 19.4 + - - +
671G GLY* 3.6 6.7 - - - +
673G LEU* 1.3 76.6 - - - +
675G LYS* 1.3 59.8 + - - +
677G SER* 3.3 7.2 + - - -
678G LEU* 2.9 29.7 + - + +
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Residues in contact with LYS 675 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D GLU* 2.9 36.3 + - - +
497G TYR* 4.6 17.9 - - + +
501G LYS* 5.2 6.4 + - - +
542G GLU* 2.8 47.5 + - + +
544G PRO* 3.9 13.1 - - - +
551G LEU* 5.5 11.7 - - + -
671G GLY 3.0 14.9 + - - +
672G GLN* 3.4 23.9 - - - +
674G TYR* 1.3 80.7 - - - +
676G GLU* 1.3 58.1 + - - +
678G LEU* 3.4 6.2 + - - +
679G SER* 2.9 28.6 + - - -
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Residues in contact with GLU 676 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662G PRO* 4.7 15.4 - - - +
672G GLN* 2.9 20.8 + - + +
673G LEU* 3.5 16.6 - - + +
675G LYS* 1.3 78.1 - - - +
677G SER* 1.3 56.7 + - - +
679G SER* 3.0 11.1 + - - -
680G ARG* 2.9 54.4 + - + +
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Residues in contact with SER 677 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284G TYR* 3.6 31.4 + - - +
285G LEU* 3.7 9.1 + - - +
286G LEU 5.0 0.2 + - - -
673G LEU 2.9 15.8 + - - -
674G TYR* 3.6 8.5 - - - -
676G GLU* 1.3 76.8 - - - +
678G LEU* 1.3 62.4 + - - +
680G ARG* 3.2 19.1 + - - +
681G LEU* 3.1 20.6 + - - +
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Residues in contact with LEU 678 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285G LEU* 3.7 18.5 - - + +
497G TYR* 3.5 37.9 - - + -
498G THR* 3.3 36.1 - - - +
501G LYS* 3.9 19.1 - - + +
502G LEU* 5.5 0.7 - - + -
674G TYR* 2.9 20.5 + - + +
675G LYS* 3.7 5.2 - - - +
677G SER* 1.3 76.8 + - - +
679G SER* 1.3 56.0 + - - +
681G LEU* 3.2 10.3 + - + -
682G MET* 2.8 49.0 + - + +
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Residues in contact with SER 679 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501G LYS* 4.7 10.4 + - - +
675G LYS* 2.9 16.5 + - - -
676G GLU* 3.0 14.1 + - - -
678G LEU* 1.3 75.7 - - - +
680G ARG* 1.3 64.5 + - - +
682G MET* 3.4 6.3 + - - +
683G ALA* 2.9 23.6 + - - +
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Residues in contact with ARG 680 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284G TYR* 4.6 14.4 - - + -
453G ARG* 5.2 14.6 - - - +
676G GLU* 2.9 40.2 + - + +
677G SER* 3.2 15.7 + - - +
679G SER* 1.3 76.3 - - - +
681G LEU* 1.3 57.1 + - - +
683G ALA* 3.1 9.3 + - - +
684G THR* 2.9 34.5 + - + +
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Residues in contact with LEU 681 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263G GLY* 6.2 1.1 - - - -
265G PHE* 4.8 7.0 - - + -
284G TYR* 3.5 45.7 - - + -
285G LEU* 4.2 14.1 - - + +
477G LEU* 4.7 17.5 - - + -
479G ILE* 5.1 9.9 - - + -
498G THR* 5.2 0.4 - - - +
502G LEU* 5.2 4.5 - - + -
677G SER 3.1 9.6 + - - +
678G LEU* 3.5 16.8 - - + +
680G ARG* 1.3 79.6 - - - +
682G MET* 1.3 58.4 + - + +
684G THR* 2.6 28.9 + - - +
685G LEU* 2.9 41.7 + - + +
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Residues in contact with MET 682 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501G LYS* 3.4 57.4 - - + +
502G LEU* 4.0 22.4 - - - -
504G GLN* 5.2 4.0 - - - +
505G LEU* 4.2 23.1 - - + +
678G LEU* 2.8 34.1 + - + +
679G SER* 3.9 5.8 - - - +
681G LEU* 1.3 76.1 - - - +
683G ALA* 1.3 58.4 + - - +
685G LEU* 4.1 5.3 - - - +
686G SER* 2.9 32.9 + - - -
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Residues in contact with ALA 683 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679G SER 2.9 14.6 + - - +
680G ARG* 3.4 10.8 - - - +
682G MET* 1.3 74.1 - - - +
684G THR* 1.3 65.5 + - + +
686G SER* 3.2 6.5 + - - -
687G ASN* 2.9 34.9 + - - +
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Residues in contact with THR 684 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G PHE* 5.1 6.8 - - - -
267G ARG* 4.7 13.7 - - - +
284G TYR* 3.9 23.9 - - + +
473G PHE* 5.3 3.8 - - - -
680G ARG* 2.9 17.2 + - + +
681G LEU* 2.6 31.4 + - - +
683G ALA* 1.3 77.1 - - + +
685G LEU* 1.3 69.5 + - - +
687G ASN* 3.2 23.7 + - - +
688G THR* 3.7 10.6 + - - +
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Residues in contact with LEU 685 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193G SER* 3.9 16.4 - - - +
195G LEU* 4.1 13.0 - - + -
265G PHE* 3.4 37.0 - - + -
477G LEU* 3.8 25.4 - - + -
502G LEU* 3.9 19.3 - - + -
505G LEU* 4.1 21.6 - - + +
681G LEU* 2.9 26.3 + - + +
682G MET* 4.1 5.6 - - - +
684G THR* 1.3 83.6 + - - +
686G SER* 1.3 58.0 + - - +
688G THR* 2.9 33.1 + - - +
690G PRO* 4.9 2.1 - - + +
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Residues in contact with SER 686 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505G LEU* 4.6 20.0 - - - +
682G MET* 2.9 23.3 + - - -
683G ALA* 3.5 7.0 - - - -
685G LEU* 1.3 76.7 - - - +
687G ASN* 1.3 63.1 - - - +
688G THR 3.3 6.1 + - - +
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Residues in contact with ASN 687 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G GLU* 5.1 6.6 - - - +
191G ASP* 5.8 0.5 + - - +
473G PHE* 6.2 0.7 - - + -
683G ALA* 2.9 29.9 + - - +
684G THR* 3.4 13.1 - - - +
685G LEU 3.1 0.4 - - - -
686G SER* 1.3 77.6 - - - +
688G THR* 1.3 63.7 + - + +
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Residues in contact with THR 688 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G GLU* 5.7 2.7 - - - -
191G ASP* 3.4 40.8 - - + +
192G GLN 4.1 0.4 - - - -
193G SER* 2.4 31.3 + - - +
265G PHE* 6.2 0.2 - - + -
473G PHE* 3.8 19.5 - - + -
684G THR 3.9 9.0 - - - +
685G LEU 2.9 17.6 + - - +
686G SER 3.6 5.7 - - - +
687G ASN* 1.3 86.4 - - + +
689G ASN* 1.3 60.7 + - - +
690G PRO* 3.3 8.1 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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