Contacts of the helix formed by residues 55 - 66 (chain C) in PDB entry 6C9G
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 GLN 55 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246B ASP 5.8 0.3 - - - +
248B VAL* 6.1 2.0 - - + -
269B PRO* 5.8 0.6 - - - +
53C SER 3.7 3.0 + - - -
54C LEU* 1.3 76.1 - - + +
56C VAL* 1.3 67.1 + - - +
57C LYS* 3.7 34.3 - - - +
58C LYS* 3.0 28.2 + - + +
59C ALA 3.2 8.3 + - - -
109C GLU* 2.7 30.1 + - - +
110C GLU 4.7 2.9 - - - +
111C HIS 3.4 12.6 - - - +
112C LYS* 4.1 6.0 - - + +
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Residues in contact with VAL 56 (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 LEU 3.2 5.3 + - - -
55C GLN* 1.3 71.8 - - - +
57C LYS* 1.3 64.3 + - - +
59C ALA* 3.4 3.1 + - - +
60C PHE* 3.2 47.0 + - + -
85C LEU* 4.9 8.1 - - + -
93C ILE* 4.0 22.2 - - + -
107C GLU 4.3 1.1 - - - +
108C LEU* 3.5 20.2 - - + +
111C HIS* 2.9 30.0 + - + +
112C LYS 4.2 2.2 - - - +
113C ILE* 4.1 30.7 - - + +
116C TRP* 5.1 5.6 - - + -
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Residues in contact with LYS 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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55C GLN* 3.2 24.0 - - - +
56C VAL* 1.3 80.3 - - - +
58C LYS* 1.3 67.6 + - - +
59C ALA 3.2 0.2 + - - -
60C PHE* 3.3 6.1 + - + +
61C PHE* 3.1 49.9 + - + -
108C LEU* 3.4 33.4 + - + +
109C GLU* 3.1 39.4 + - + +
254C TYR* 3.9 15.0 + - + +
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Residues in contact with LYS 58 (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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245B LYS* 3.7 15.7 + - - +
246B ASP* 3.2 28.9 + - + +
248B VAL* 3.9 28.9 - - + -
250B VAL* 5.9 1.1 - - - -
267B TYR* 5.0 13.0 - - + -
54C LEU* 4.0 20.0 - - + -
55C GLN* 3.0 24.8 + - + +
57C LYS* 1.3 80.9 - - - +
59C ALA* 1.3 57.9 + - - +
61C PHE* 3.4 15.4 + - + +
62C ALA* 3.0 25.8 + - - +
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Residues in contact with ALA 59 (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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50C PHE* 3.3 18.0 - - + -
54C LEU* 3.8 23.7 - - + +
55C GLN 3.2 6.3 + - - +
56C VAL 3.6 10.1 - - - +
57C LYS 3.1 0.4 - - - -
58C LYS* 1.3 74.2 - - - +
60C PHE* 1.3 65.5 + - - +
62C ALA* 3.0 13.0 + - - +
63C LEU* 3.0 12.6 + - - +
85C LEU* 3.7 23.6 - - + -
113C ILE* 4.0 9.9 - - + -
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Residues in contact with PHE 60 (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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56C VAL* 3.2 35.3 + - + -
57C LYS* 3.3 7.1 + - + +
59C ALA* 1.3 76.4 - - - +
61C PHE* 1.3 65.4 + - + +
63C LEU* 3.6 18.7 + - + +
64C VAL* 3.4 24.8 + - - +
85C LEU* 4.0 27.1 - - + -
86C THR 3.5 17.9 - - - -
89C ASP* 3.8 5.4 - - + -
90C PHE* 3.4 66.9 - + + -
93C ILE* 4.1 11.4 - - + -
108C LEU* 4.3 7.4 - - + -
246C ILE* 4.8 6.9 - - + +
249C ALA* 4.4 7.7 - - + +
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Residues in contact with PHE 61 (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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57C LYS* 3.1 49.6 + - + -
58C LYS* 3.6 16.4 - - + +
60C PHE* 1.3 79.3 - - + +
62C ALA* 1.3 60.6 + - - +
64C VAL* 3.0 8.8 + - + +
65C THR* 2.8 32.8 + - - +
90C PHE* 6.5 0.2 - + - -
249C ALA* 3.5 35.9 - - + -
252C LYS* 4.2 30.7 - - + -
254C TYR* 4.2 14.4 - + - -
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Residues in contact with ALA 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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267B TYR* 3.6 29.6 - - + -
48C VAL* 5.2 1.1 - - + -
50C PHE* 3.6 22.9 - - + -
58C LYS 3.0 14.2 + - - +
59C ALA* 3.0 10.1 + - - +
61C PHE* 1.3 77.2 - - - +
63C LEU* 1.3 57.1 + - - +
65C THR* 3.1 8.4 + - - -
66C ASN* 2.8 36.0 + - - +
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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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48C VAL* 5.2 4.3 - - + -
50C PHE* 3.8 24.0 - - + -
59C ALA 3.0 14.8 + - - +
60C PHE* 3.7 32.5 - - + +
61C PHE 3.3 0.2 - - - -
62C ALA* 1.3 76.0 - - - +
64C VAL* 1.3 58.5 + - + +
66C ASN* 5.3 1.6 - - - -
67C GLY* 3.1 6.9 + - - -
68C VAL* 2.9 48.6 + - + +
69C ARG 3.7 17.9 - - - +
70C ALA 4.0 10.5 - - - +
71C ALA* 3.9 15.3 - - + -
85C LEU* 4.1 13.7 - - + +
86C THR 4.9 2.9 - - - -
87C ILE* 5.2 4.3 - - + +
246C ILE* 5.4 6.5 - - + -
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Residues in contact with VAL 64 (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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60C PHE 3.4 15.0 + - - +
61C PHE* 3.0 10.2 + - + +
63C LEU* 1.3 75.1 - - - +
65C THR* 1.3 69.2 + - - +
67C GLY* 3.1 13.5 + - - -
246C ILE* 3.9 30.1 - - + +
249C ALA* 4.0 16.8 - - + -
250C ALA* 4.0 24.7 - - + +
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Residues in contact with THR 65 (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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395A LYS* 2.7 36.8 + - + +
396A ALA* 5.4 9.0 - - + -
267B TYR* 4.6 5.6 - - - +
61C PHE* 2.8 21.4 + - - +
62C ALA* 3.4 12.0 - - - -
64C VAL* 1.3 77.0 - - - +
66C ASN* 1.3 66.4 + - - +
67C GLY* 3.4 0.5 + - - -
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Residues in contact with ASN 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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395A LYS* 4.2 12.1 - - - +
398A TRP* 5.6 2.4 - - - +
225B PRO* 4.6 4.5 - - - +
265B LEU* 3.5 24.8 - - - +
267B TYR* 2.7 35.7 + - - -
46C LYS* 3.2 32.1 + - - +
48C VAL* 3.8 21.7 - - + +
62C ALA 2.8 20.7 + - - +
63C LEU* 4.7 0.9 - - - +
65C THR* 1.3 74.7 - - - +
67C GLY* 1.3 63.1 + - - +
68C VAL* 3.3 8.4 - - + +
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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