Contacts of the helix formed by residues 665 - 676 (chain N) in PDB entry 5GJQ
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 ASN 665 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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630N PRO* 5.7 6.1 - - - -
631N GLU* 5.7 4.9 - - - -
634N PRO* 5.3 3.8 - - - -
660N CYS* 4.1 8.7 - - - -
664N GLY* 1.3 76.7 - - - +
666N LYS* 1.3 57.7 + - - +
667N GLU* 2.9 26.5 - - + -
668N ALA* 2.8 15.7 + - + +
669N ILE* 2.7 32.1 + - - +
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Residues in contact with LYS 666 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664N GLY 3.8 1.0 - - - -
665N ASN* 1.3 71.0 - - - +
667N GLU* 1.3 56.9 + - - +
669N ILE* 3.5 16.5 - - + +
670N ASN* 2.4 50.3 + - - -
702N THR 5.4 1.8 - - - +
703N CYS* 3.8 31.2 - - + -
704N PRO* 6.4 0.4 - - + -
705N LYS* 5.6 8.1 - - + -
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Residues in contact with GLU 667 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634N PRO* 5.1 7.1 - - + +
665N ASN* 3.1 33.7 - - + -
666N LYS* 1.3 78.4 - - - +
668N ALA* 1.3 76.7 + - - +
670N ASN* 3.3 5.9 + - - +
671N LEU* 3.2 16.5 + - - +
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Residues in contact with ALA 668 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634N PRO* 3.3 35.4 - - + +
656N LEU* 3.6 27.4 - - + +
660N CYS* 4.1 7.4 - - + -
664N GLY 4.7 0.2 - - - +
665N ASN* 2.8 21.7 + - + +
667N GLU* 1.3 83.3 - - - +
669N ILE* 1.3 66.0 + - + +
671N LEU* 3.2 15.0 + - - +
672N LEU* 3.7 2.5 + - - +
694N ILE* 5.3 1.8 - - + -
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Residues in contact with ILE 669 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664N GLY 5.5 0.2 - - - -
665N ASN 2.7 21.4 + - - +
666N LYS* 3.1 19.3 - - + +
668N ALA* 1.3 72.1 - - - +
670N ASN* 1.3 59.8 + - - +
672N LEU* 2.6 41.0 + - + +
673N GLU* 3.5 12.5 + - + -
691N SER* 4.2 20.2 - - - +
694N ILE* 3.5 46.0 - - + -
695N MET* 4.1 18.2 - - + -
698N GLN* 5.4 1.8 - - - +
703N CYS* 6.5 0.4 - - - -
705N LYS* 5.5 10.8 - - + -
709N PHE* 5.6 5.2 - - + -
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Residues in contact with ASN 670 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666N LYS* 2.4 50.0 + - - +
667N GLU* 3.8 5.6 - - - +
669N ILE* 1.3 71.4 - - - +
671N LEU* 1.3 61.7 + - - +
673N GLU* 3.3 15.8 + - - +
674N PRO* 3.0 20.1 - - - +
705N LYS* 5.1 13.0 - - - -
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Residues in contact with LEU 671 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634N PRO* 5.1 5.6 - - + +
637N VAL* 4.6 14.8 - - + -
638N SER* 5.0 6.7 - - - +
641N SER* 3.8 28.9 - - - +
656N LEU* 4.8 2.0 - - + -
667N GLU 3.2 9.9 + - - +
668N ALA* 3.2 15.4 + - - +
669N ILE 2.9 0.8 + - - -
670N ASN* 1.3 74.9 - - - +
672N LEU* 1.3 66.7 + - + +
674N PRO* 3.2 18.8 - - - +
675N MET* 4.1 5.6 + - + +
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Residues in contact with LEU 672 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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637N VAL* 5.5 1.6 - - + -
641N SER* 6.3 0.9 - - - -
652N ALA* 4.9 6.1 - - + -
653N ALA* 4.0 26.7 - - + +
656N LEU* 4.3 19.5 - - + -
657N GLY* 4.6 4.9 - - - +
668N ALA 3.9 9.0 - - - +
669N ILE* 2.6 24.5 + - - +
671N LEU* 1.3 76.4 - - + +
673N GLU* 1.3 49.8 + - - -
675N MET* 2.7 22.0 + - + +
676N THR* 2.6 35.5 + - - +
687N ALA* 4.6 6.5 - - + +
690N ALA* 3.9 28.3 - - + -
691N SER* 4.5 19.7 - - - +
694N ILE* 5.1 2.5 - - + -
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Residues in contact with GLU 673 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669N ILE* 4.1 13.2 - - + +
670N ASN* 3.3 21.5 + - + +
672N LEU* 1.3 76.7 - - - +
674N PRO* 1.3 70.3 - - + +
676N THR* 2.1 36.9 + - + +
677N ASN* 3.2 7.3 + - - -
691N SER* 5.5 2.5 - - - +
705N LYS* 6.2 2.7 - - + -
709N PHE* 5.4 11.0 - - + -
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Residues in contact with PRO 674 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670N ASN 3.0 27.4 - - - +
671N LEU* 3.2 11.4 - - - +
673N GLU* 1.3 79.3 - - + +
675N MET* 1.3 53.7 + - + +
677N ASN* 2.6 30.0 + - + +
678N ASP* 3.1 8.8 + - - +
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Residues in contact with MET 675 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641N SER* 4.4 24.9 - - - +
649N ARG* 4.5 21.8 - - + +
652N ALA* 5.7 1.3 - - + -
653N ALA* 6.0 0.9 - - + -
671N LEU 4.4 9.4 - - - +
672N LEU* 2.7 29.6 + - + +
674N PRO* 1.3 71.6 - - + +
676N THR* 1.3 55.2 + - - -
677N ASN 2.9 4.9 - - - -
678N ASP* 2.8 30.0 + - - +
683N VAL* 3.7 9.1 - - + +
684N ARG* 3.6 10.2 - - - -
687N ALA* 4.1 11.2 - - + -
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Residues in contact with THR 676 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672N LEU 2.6 23.0 + - - +
673N GLU* 2.1 40.8 + - + +
675N MET* 1.3 72.1 - - - +
677N ASN* 1.3 58.0 + - - +
684N ARG* 2.7 44.2 + - - +
687N ALA* 3.5 23.6 - - + +
688N LEU* 4.5 7.0 - - + +
691N SER* 4.6 7.9 - - - +
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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