Contacts of the helix formed by residues 56 - 70 (chain C) in PDB entry 6GYS
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 GLU 56 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C SER* 3.3 12.1 + - - +
55C LYS* 1.3 75.9 - - - +
57C TYR* 1.3 62.5 + - - +
58C LEU 3.3 0.2 - - - -
59C PRO* 3.7 10.4 - - + +
60C ASP* 3.6 21.5 + - - +
531C ASP* 3.9 17.3 - - - +
533C PHE* 3.2 36.0 - - + -
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Residues in contact with TYR 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C SER 3.4 24.9 - - - -
55C LYS* 3.7 25.0 - - + +
56C GLU* 1.3 79.4 - - - +
58C LEU* 1.3 78.5 + - + +
60C ASP* 3.7 5.3 + - - +
61C LEU* 2.8 42.8 + - + +
476C PHE* 4.5 22.3 + - + +
477C VAL* 5.1 5.4 - - - +
521C TRP* 4.2 24.9 + + - -
526C LEU* 3.9 18.8 - - + -
533C PHE* 3.2 25.1 - + + -
538C PHE* 4.2 11.0 - - + -
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Residues in contact with LEU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LYS* 3.6 13.6 + - + +
57C TYR* 1.3 101.2 - - + +
59C PRO* 1.4 68.2 - - + +
61C LEU* 4.2 7.0 - - + -
62C LEU* 2.9 48.0 + - + +
472C PHE* 5.9 2.9 - - + -
473C TYR* 5.8 7.4 - - + -
476C PHE* 4.9 8.3 - - + -
477C VAL* 4.1 31.2 - - + -
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Residues in contact with PRO 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LYS 3.3 17.0 - - - +
56C GLU* 3.7 10.1 - - + +
58C LEU* 1.4 89.7 - - + +
60C ASP* 1.3 57.5 + - - +
62C LEU* 3.3 11.6 + - + +
63C LEU* 2.9 38.5 + - + +
420C ILE 5.8 1.3 - - - +
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Residues in contact with ASP 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLU* 3.6 25.6 + - - +
57C TYR* 3.7 6.4 - - - +
59C PRO* 1.3 82.2 - - - +
61C LEU* 1.3 60.4 + - - +
63C LEU* 3.3 10.4 + - - +
64C PHE* 2.8 26.5 + - - +
533C PHE* 6.2 1.1 - - + -
538C PHE* 5.7 5.2 - - - -
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Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C TYR* 2.8 26.3 + - + +
58C LEU* 3.7 8.1 - - + +
59C PRO 3.2 0.4 - - - -
60C ASP* 1.3 77.7 - - - +
62C LEU* 1.3 61.6 + - - +
64C PHE* 3.2 27.7 + - + +
65C TRP 2.8 22.0 + - - -
472C PHE* 3.2 25.7 - - + -
476C PHE* 3.6 46.2 - - + -
538C PHE* 3.7 31.2 - - + -
541C LEU* 4.9 4.3 - - + -
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Residues in contact with LEU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C LEU* 2.9 35.8 + - + +
59C PRO* 3.6 10.3 - - + +
61C LEU* 1.3 78.5 - - - +
63C LEU* 1.3 60.2 + - + +
65C TRP* 3.2 17.8 + - - +
66C GLN* 3.5 6.1 + - - +
419C LEU* 4.1 9.4 - - + +
420C ILE* 3.7 63.5 - - + +
469C PHE* 4.4 9.9 - - + -
472C PHE* 3.6 23.6 - - + -
473C TYR* 5.8 6.1 - - + -
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Residues in contact with LEU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C PRO* 2.9 25.3 + - + +
60C ASP* 3.7 8.7 - - - +
62C LEU* 1.3 74.7 - - - +
64C PHE* 1.3 64.7 + - - +
65C TRP 3.5 0.2 + - - -
66C GLN* 3.5 18.0 + - + +
67C ASN* 3.9 5.5 + - - +
362C SER* 5.1 15.6 - - - +
364C LYS* 4.7 21.5 - - - +
420C ILE* 4.5 10.1 - - + +
421C TYR* 4.1 31.0 - - + -
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Residues in contact with PHE 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ASP* 2.8 17.1 + - - +
61C LEU* 3.2 30.9 + - + +
63C LEU* 1.3 77.0 - - - +
65C TRP* 1.3 59.7 + - - +
66C GLN 3.2 0.2 + - - -
67C ASN* 3.3 6.6 + - + +
68C TYR* 2.9 48.9 + + + +
472C PHE* 5.2 3.8 - + - -
538C PHE 5.1 0.2 - - - -
541C LEU* 3.2 47.6 - - + -
542C GLN* 3.2 25.8 - - - -
545C ILE* 3.6 22.4 - - + -
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Residues in contact with TRP 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU 2.8 14.0 + - - +
62C LEU* 3.2 12.0 + - - +
64C PHE* 1.3 77.1 - - - +
66C GLN* 1.3 60.3 + - - +
68C TYR* 3.3 41.5 - + - +
69C GLU* 2.5 63.4 + - - +
73C THR* 4.5 4.3 - - + -
416C LYS* 3.4 8.3 - - - +
420C ILE* 3.5 25.4 - - + -
465C ARG 4.4 2.0 - - - -
468C SER* 3.4 34.1 - - - -
469C PHE* 3.5 29.9 - + + -
472C PHE* 3.5 45.5 - + + -
514C LEU* 6.1 1.3 - - + -
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Residues in contact with GLN 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C LEU 3.8 10.8 - - - +
63C LEU* 3.7 12.8 - - + +
64C PHE 3.1 0.6 - - - -
65C TRP* 1.3 83.3 - - - +
67C ASN* 1.3 58.0 + - - +
69C GLU* 3.1 7.0 + - - +
70C TYR 2.9 23.7 + - - -
358C TYR* 3.6 18.6 + - - +
359C LEU* 3.0 28.0 - - - +
361C LYS 5.4 2.2 - - - +
362C SER* 6.1 2.7 - - - -
416C LYS* 3.7 9.6 + - - +
417C MET* 5.4 4.3 - - - +
420C ILE* 3.5 26.6 - - + +
421C TYR* 2.7 41.3 + - + +
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Residues in contact with ASN 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C LEU 3.9 5.7 + - - +
64C PHE* 3.3 9.2 + - + +
66C GLN* 1.3 75.8 - - - +
68C TYR* 1.3 65.6 + - - +
70C TYR* 3.9 7.2 - - - +
71C TRP* 3.1 43.0 + - - +
359C LEU 3.9 5.9 + - - -
360C ASN* 4.9 8.3 - - - +
545C ILE* 3.8 14.0 - - + +
549C GLU* 4.6 1.4 + - - +
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Residues in contact with TYR 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C PHE* 2.9 42.9 + + + +
65C TRP* 3.3 42.6 - + - +
67C ASN* 1.3 76.8 - - - +
69C GLU* 1.3 55.5 + - - +
71C TRP 3.0 2.6 + - - -
72C ILE* 2.6 75.9 + - + +
73C THR* 4.6 5.6 - - + -
468C SER* 5.7 1.8 - - - -
472C PHE* 6.0 1.3 - + - -
510C LEU* 4.7 4.0 - - + +
513C ARG* 5.7 1.0 + - - -
514C LEU* 3.5 26.9 - - + +
541C LEU* 3.6 29.7 - - + +
544C ASP* 4.3 7.4 + - - -
545C ILE* 3.7 10.0 - - + +
603C ILE* 6.0 0.2 - - - +
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Residues in contact with GLU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C TRP* 2.5 61.1 + - + +
66C GLN* 3.7 6.5 - - - +
68C TYR* 1.3 71.7 - - - +
70C TYR* 1.3 64.0 + - - +
71C TRP 3.3 0.2 + - - -
73C THR* 2.4 48.5 + - + +
74C ASN* 3.3 7.8 - - - +
359C LEU* 5.2 15.5 - - + +
412C TRP* 4.6 1.0 - - - -
413C LYS* 5.3 2.1 - - - -
416C LYS* 3.2 21.9 + - - -
465C ARG* 3.1 34.9 + - - +
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Residues in contact with TYR 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C GLN 2.9 6.3 + - - +
67C ASN* 4.0 5.8 - - - +
68C TYR 3.2 0.6 - - - -
69C GLU* 1.3 78.7 - - - +
71C TRP* 1.3 100.5 + + + +
74C ASN* 3.0 33.4 + - - +
75C ILE* 3.3 9.3 - - + +
304C SER 6.2 0.4 - - - -
305C GLY* 5.6 2.4 - - - -
306C PRO* 4.9 14.2 - - + +
359C LEU* 3.3 46.2 - - + +
360C ASN* 3.2 42.7 + - + -
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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