Contacts of the helix formed by residues 55 - 70 (chain C) in PDB entry 1SHZ
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 ARG 55 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C GLN* 4.0 9.6 - - - +
51C GLN* 4.4 10.8 - - - +
52C VAL* 2.8 16.8 + - + +
54C ARG* 1.3 116.6 + - - +
56C PRO* 1.3 64.9 - - + +
57C ALA 3.5 0.2 - - - -
58C HIS* 3.5 35.4 - - + -
59C LEU* 3.1 23.2 + - - +
183C ARG* 3.7 27.5 - - - +
186C TYR* 4.4 8.6 - - - -
187C GLU* 4.6 8.1 + - - +
190C GLU* 3.0 33.6 + - - +
229C LEU* 4.9 1.1 - - - -
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Residues in contact with PRO 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ARG 3.1 12.3 - - - +
55C ARG* 1.3 80.9 - - + +
57C ALA* 1.3 70.3 + - - +
59C LEU* 3.6 3.8 + - + +
60C MET* 3.1 27.4 + - - +
190C GLU* 3.8 39.7 - - + +
191C ARG* 4.5 6.7 - - + +
194C ALA* 4.1 16.1 - - + +
226C MET* 4.2 3.4 - - + +
229C LEU* 3.8 28.7 - - + -
231C VAL* 4.5 9.2 - - + -
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Residues in contact with ALA 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 ARG 3.5 0.4 - - - -
56C PRO* 1.3 81.1 - - - +
58C HIS* 1.3 68.0 + - + +
60C MET* 2.9 17.3 + - - +
61C ALA* 3.3 9.5 + - - +
172C LEU* 4.2 8.9 - - + +
175C LEU* 3.6 31.0 - - + -
190C GLU* 4.3 14.1 - - + +
193C VAL* 4.3 16.4 - - + -
194C ALA* 4.3 7.8 - - - +
197C LEU* 4.2 6.1 - - + +
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Residues in contact with HIS 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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45C GLN* 3.1 39.1 + - + +
46C PHE* 3.5 19.1 - - + -
52C VAL* 3.8 12.6 - - + -
55C ARG* 3.5 32.0 + - + -
56C PRO 3.5 0.2 - - - -
57C ALA* 1.3 80.3 - - + +
59C LEU* 1.3 61.5 + - - +
61C ALA* 3.1 14.2 + - - +
62C LEU 3.2 8.3 + - - -
161C ARG* 5.3 0.6 + - - -
172C LEU* 3.8 32.7 - - + +
175C LEU* 5.2 6.3 - - + +
176C GLU* 4.1 25.5 - - + +
186C TYR* 4.4 12.9 + - - -
190C GLU* 4.5 5.1 + - - -
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Residues in contact with LEU 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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49C LEU* 4.7 2.9 - - + -
52C VAL* 3.8 35.0 - - + +
53C LYS* 4.3 8.5 - - - +
55C ARG 3.1 20.0 + - - +
56C PRO 3.7 4.7 - - - +
58C HIS* 1.3 78.2 - - - +
60C MET* 1.3 52.4 + - - +
62C LEU* 3.1 9.8 + - + +
63C LEU* 2.5 55.7 + - + +
79C LEU* 3.8 15.9 - - + -
225C TYR* 3.4 35.0 - - + -
226C MET* 3.6 16.6 - - + -
229C LEU* 4.8 0.7 - - + -
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Residues in contact with MET 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C PRO 3.1 17.3 + - - +
57C ALA* 2.9 10.8 + - - +
59C LEU* 1.3 76.6 - - - +
61C ALA* 1.3 61.4 + - - +
63C LEU* 4.0 7.6 - - + -
64C GLN* 3.3 24.8 + - - +
168C TRP* 4.6 1.3 - - - +
194C ALA* 4.1 17.5 - - - +
197C LEU* 3.8 19.7 - - + -
198C LEU* 3.5 37.2 - - + +
201C LEU* 3.7 28.0 - - + -
222C ILE* 4.2 18.8 - - + -
226C MET* 3.9 23.6 - - - +
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Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ALA 3.3 2.8 + - - -
58C HIS 3.1 10.7 + - - +
59C LEU 3.1 1.0 - - - -
60C MET* 1.3 76.6 - - - +
62C LEU* 1.3 63.9 + - - +
64C GLN* 3.6 4.6 + - - +
65C HIS* 3.3 20.6 + - - +
157C PHE* 3.8 22.1 - - + -
167C PRO* 4.6 13.6 - - - +
168C TRP* 4.6 12.1 - - + -
172C LEU* 3.9 31.4 - - + -
197C LEU* 5.0 0.6 - - + +
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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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46C PHE* 4.1 8.1 - - + -
49C LEU* 4.4 9.0 - - + -
52C VAL* 4.1 19.7 - - + -
58C HIS 3.2 7.2 + - - +
59C LEU* 3.1 16.8 + - + +
61C ALA* 1.3 76.3 - - - +
63C LEU* 1.3 66.4 + - - +
64C GLN 3.0 3.0 + - - -
65C HIS* 3.0 5.6 + - + +
66C VAL* 3.0 39.1 + - + +
75C LEU* 4.2 14.4 - - + -
153C GLN* 4.7 1.1 - - + +
154C LEU* 3.5 39.0 - - + +
157C PHE* 3.9 29.3 - - + -
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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 LEU* 2.5 50.4 + - + +
60C MET* 4.1 13.5 - - + +
62C LEU* 1.3 72.9 - - - +
64C GLN* 1.3 60.3 + - - +
67C ALA* 3.1 29.3 + - + +
72C PRO* 6.2 1.3 - - + -
75C LEU* 3.9 22.2 - - + -
76C LEU* 3.9 16.2 - - + -
79C LEU* 3.6 19.5 - - + -
201C LEU* 4.7 1.7 - - - +
218C VAL* 5.6 0.2 - - + -
222C ILE* 3.5 45.9 - - + +
226C MET* 6.0 1.1 - - + -
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Residues in contact with GLN 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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280A TRP* 5.6 6.8 + - - -
60C MET 3.3 14.3 + - - +
61C ALA 3.7 3.8 + - - +
62C LEU 3.0 0.8 - - - -
63C LEU* 1.3 77.1 - - - +
65C HIS* 1.3 69.7 + - - +
66C VAL 3.2 0.2 + - - -
67C ALA* 3.3 2.0 + - - +
68C LEU* 2.9 38.2 + - + +
167C PRO* 3.3 27.8 - - + +
168C TRP* 2.7 46.7 + - - +
201C LEU* 3.5 27.8 - - + +
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Residues in contact with HIS 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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61C ALA 3.3 10.3 + - - +
62C LEU* 3.0 7.6 + - - +
64C GLN* 1.3 80.2 - - - +
66C VAL* 1.3 61.7 + - + +
68C LEU* 3.8 2.0 - - - -
69C GLN* 2.8 52.3 + - + +
70C PHE* 3.7 19.2 - + - -
153C GLN 4.9 1.1 - - - -
156C ASP* 2.9 24.1 + - - -
157C PHE* 3.8 34.2 - + + -
160C LYS* 3.7 27.6 - - + +
165C MET 4.8 5.1 + - - -
166C THR* 4.9 2.8 - - - +
167C PRO* 4.9 10.9 - - + +
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Residues in contact with VAL 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* 3.0 28.7 + - + +
63C LEU* 4.4 1.1 - - + +
65C HIS* 1.3 73.1 - - + +
67C ALA* 1.3 66.3 + - - +
68C LEU 2.8 2.0 + - - -
70C PHE* 2.7 41.9 + - + +
71C GLU 4.1 15.7 - - - +
72C PRO* 4.3 8.1 - - + -
75C LEU* 3.6 29.2 - - + -
153C GLN* 3.2 41.3 - - + +
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Residues in contact with ALA 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* 3.1 22.2 + - + +
64C GLN* 3.8 3.8 - - - +
66C VAL* 1.3 79.5 - - - +
68C LEU* 1.3 61.4 + - + +
70C PHE 3.9 6.9 - - - +
72C PRO* 4.3 17.0 - - + +
201C LEU* 5.5 5.4 - - + -
208C ILE* 3.5 32.7 - - + +
218C VAL* 4.2 25.1 - - + -
222C ILE* 4.8 3.6 - - + -
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Residues in contact with LEU 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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279A LYS* 3.1 23.7 - - + +
280A TRP* 3.9 20.0 - - + +
64C GLN* 2.9 28.4 + - + +
65C HIS* 3.9 2.5 - - - +
66C VAL 2.8 0.4 + - - -
67C ALA* 1.3 80.7 - - + +
69C GLN* 1.3 79.1 + - + +
70C PHE 4.6 0.5 - - - +
201C LEU* 6.4 2.7 - - + -
204C MET 6.1 0.2 - - - +
205C GLN* 5.4 4.3 - - - +
207C THR* 3.3 56.9 - - + +
208C ILE* 3.9 16.0 - - + +
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Residues in contact with GLN 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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277A ASN 4.0 4.0 - - - +
278A ASN* 3.0 30.7 + - - +
279A LYS* 3.1 46.3 + - + +
280A TRP* 4.1 3.8 - - - +
65C HIS* 2.8 44.3 + - + +
68C LEU* 1.3 102.8 - - + +
70C PHE* 1.3 79.9 + - + +
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Residues in contact with PHE 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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279A LYS* 5.3 2.1 - - - -
65C HIS* 3.7 25.4 - + - -
66C VAL* 2.7 36.4 + - + +
67C ALA 3.9 5.7 - - - +
68C LEU 4.6 1.0 - - - +
69C GLN* 1.3 86.5 - - + +
71C GLU* 1.3 74.2 + - - +
72C PRO* 3.6 5.2 - - - +
152C ARG 5.6 0.9 - - - -
153C GLN* 3.6 43.1 - - + +
156C ASP* 3.3 36.8 - - + -
208C ILE 5.5 1.4 - - - +
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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
------------------------------------------------------------
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