Contacts of the helix formed by residues 55 - 70 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51F GLN 3.6 16.2 + - - +
52F VAL* 3.0 9.0 + - - +
54F ARG* 1.3 126.8 + - - +
56F PRO* 1.3 62.8 - - - +
57F ALA 3.4 0.7 - - - +
58F HIS* 3.8 33.2 - - + -
59F LEU* 3.0 29.6 + - - +
186F TYR* 5.4 1.8 - - - -
187F GLU* 5.3 6.3 - - - +
190F GLU* 2.7 37.7 + - - +
229F LEU* 5.0 0.7 - - - -
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Residues in contact with PRO 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F ARG 3.2 11.6 - - - +
55F ARG* 1.3 81.8 - - - +
57F ALA* 1.3 63.1 + - - +
59F LEU* 3.8 3.2 - - + +
60F MET* 3.1 26.9 + - - +
190F GLU* 3.3 39.9 - - + +
191F ARG* 3.9 14.6 - - + -
194F ALA* 3.5 17.0 - - + -
226F MET* 3.7 7.7 - - + +
229F LEU* 4.5 16.6 - - + -
231F VAL* 3.7 16.2 - - + -
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Residues in contact with ALA 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F ARG 3.4 0.4 - - - -
56F PRO* 1.3 77.6 - - - +
58F HIS* 1.3 71.5 + - + +
60F MET* 2.9 20.6 + - - +
61F ALA 3.3 4.0 + - - -
172F LEU* 4.1 13.0 - - + +
175F LEU* 4.0 22.7 - - + -
190F GLU* 3.8 17.0 - - + +
193F VAL* 4.4 14.4 - - + -
194F ALA* 3.8 10.0 - - - +
197F LEU* 3.9 8.2 - - + +
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Residues in contact with HIS 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F GLN* 3.4 18.5 + - + +
46F PHE* 3.1 34.4 - + + -
52F VAL* 3.7 17.9 - - + -
55F ARG* 3.7 30.2 + - + -
57F ALA* 1.3 84.3 - - + +
59F LEU* 1.3 63.9 + - - +
61F ALA* 3.3 3.3 + - - +
62F LEU 3.2 9.0 + - - -
172F LEU* 3.4 25.9 - - + +
175F LEU* 5.7 3.8 - - + +
176F GLU* 3.4 39.3 - - + +
186F TYR* 4.7 9.6 + - - -
190F GLU* 4.7 5.8 - - + -
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Residues in contact with LEU 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F LEU* 5.2 1.6 - - + -
52F VAL* 3.7 18.5 - - + +
53F LYS* 4.1 14.1 - - - +
55F ARG 3.0 20.8 + - - +
56F PRO 3.8 3.1 - - - +
58F HIS* 1.3 77.3 - - - +
60F MET* 1.3 62.5 + - - +
62F LEU* 3.2 23.6 + - + +
63F LEU* 2.9 49.8 + - + +
75F LEU* 5.9 0.2 - - + -
79F LEU* 4.1 13.7 - - + -
225F TYR* 3.6 36.8 - - + -
226F MET* 4.7 9.2 - - - -
229F LEU* 4.6 6.1 - - + -
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Residues in contact with MET 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F PRO 3.1 18.2 + - - +
57F ALA 2.9 11.2 + - - +
59F LEU* 1.3 76.5 - - - +
61F ALA* 1.3 52.3 + - - +
63F LEU* 3.3 6.5 + - + +
64F GLN* 2.8 37.9 + - + +
168F TRP* 4.8 2.0 - - - +
194F ALA* 3.9 15.7 - - - +
197F LEU* 3.9 19.1 - - + +
198F LEU* 3.5 33.4 - - + +
201F LEU* 3.2 34.5 - - + -
222F ILE* 4.6 6.3 - - - -
226F MET* 3.7 29.2 - - + +
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Residues in contact with ALA 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F ALA 3.3 4.5 + - - +
58F HIS 3.3 11.2 + - - +
59F LEU 3.2 0.4 - - - -
60F MET* 1.3 76.8 - - - +
62F LEU* 1.3 66.6 + - - +
64F GLN* 3.1 3.6 + - - +
65F HIS* 2.9 23.6 + - - +
157F PHE* 3.9 17.4 - - + -
167F PRO* 3.9 21.1 - - + +
168F TRP* 4.3 15.4 - - + -
172F LEU* 4.4 16.8 - - + -
197F LEU* 5.6 0.2 - - + -
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Residues in contact with LEU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F PHE* 4.2 7.9 - - + -
49F LEU* 4.6 2.9 - - + -
52F VAL* 3.8 27.4 - - + -
58F HIS 3.2 10.1 + - - +
59F LEU* 3.5 19.7 - - + +
61F ALA* 1.3 78.9 - - - +
63F LEU* 1.3 56.6 + - - +
65F HIS* 3.2 1.9 + - - +
66F VAL* 2.8 46.8 + - + +
75F LEU* 3.9 24.5 - - + -
153F GLN* 5.0 1.3 - - + +
154F LEU* 3.6 30.3 - - + +
157F PHE* 3.7 28.1 - - + -
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Residues in contact with LEU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F LEU* 2.9 57.1 + - + +
60F MET* 3.7 8.7 - - + +
62F LEU* 1.3 70.7 - - - +
64F GLN* 1.3 58.2 + - - +
65F HIS 3.0 1.6 - - - -
66F VAL* 3.6 2.9 - - + +
67F ALA* 2.7 38.5 + - - +
75F LEU* 3.4 33.9 - - + -
76F LEU* 5.0 9.9 - - + -
79F LEU* 4.3 13.9 - - + -
201F LEU* 4.8 4.9 - - + -
222F ILE* 4.5 36.8 - - + -
226F MET* 5.9 0.7 - - - -
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Residues in contact with GLN 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D TRP* 4.8 9.1 + - - +
60F MET 2.8 20.8 + - - +
61F ALA 3.6 4.5 - - - +
63F LEU* 1.3 73.7 - - - +
65F HIS* 1.3 58.0 + - - +
67F ALA* 4.2 4.5 - - - -
68F LEU* 2.9 42.5 + - - +
167F PRO* 3.7 22.9 - - + +
168F TRP* 3.5 33.1 - - + +
200F HIS 5.7 0.3 - - - +
201F LEU* 4.2 29.9 - - + +
204F MET* 5.8 3.1 - - - +
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Residues in contact with HIS 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D SER* 5.8 0.9 - - - -
61F ALA 2.9 12.0 + - - +
62F LEU 3.3 7.4 - - - +
64F GLN* 1.3 75.7 - - - +
66F VAL* 1.3 70.7 + - + +
67F ALA 3.0 4.9 + - - -
68F LEU* 3.2 4.5 + - - +
69F GLN* 3.0 44.4 + - + +
70F PHE* 3.9 10.6 - + - -
153F GLN 4.5 1.8 - - - -
156F ASP* 2.8 28.0 + - - -
157F PHE* 3.4 38.3 - + + -
160F LYS* 3.9 23.3 - - + -
165F MET 5.2 3.7 + - - -
166F THR* 4.9 1.8 - - - +
167F PRO* 4.4 13.9 - - + +
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Residues in contact with VAL 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F LEU* 2.8 31.9 + - + +
63F LEU* 4.0 3.8 - - + +
65F HIS* 1.3 79.0 - - + +
67F ALA* 1.3 56.7 - - - +
70F PHE* 3.1 37.6 + - + +
71F GLU 4.2 10.1 - - - +
72F PRO* 4.4 6.8 - - + -
75F LEU* 3.6 28.7 - - + -
153F GLN* 3.2 40.6 - - + +
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Residues in contact with ALA 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D LYS* 3.9 11.4 + - - +
63F LEU 2.7 18.1 + - - +
64F GLN* 3.7 9.2 - - - +
65F HIS 3.0 0.2 - - - -
66F VAL* 1.3 81.6 - - - +
68F LEU* 1.3 67.9 + - + +
69F GLN 3.6 0.3 + - - -
70F PHE 3.7 8.9 - - - +
72F PRO* 5.1 11.0 - - + +
201F LEU* 5.8 6.7 - - + -
208F ILE* 4.1 29.2 - - + +
218F VAL* 5.5 7.0 - - + -
222F ILE* 6.0 2.9 - - + -
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Residues in contact with LEU 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D ASN 3.5 4.9 - - - +
278D ASN* 3.6 16.0 - - - +
279D LYS* 3.2 44.3 + - + +
280D TRP* 3.3 37.2 - - + +
64F GLN* 2.9 50.3 - - - +
65F HIS* 3.2 4.1 + - - +
67F ALA* 1.3 87.1 - - + +
69F GLN* 1.3 61.4 + - + +
207F THR* 4.3 13.7 - - - +
208F ILE* 5.1 5.4 - - + -
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Residues in contact with GLN 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D ASP* 4.6 2.3 - - - +
274D SER* 2.8 46.6 + - - +
277D ASN* 3.6 22.1 - - - +
278D ASN* 3.7 27.9 - - - +
279D LYS* 4.8 7.1 - - - -
334D LYS* 4.6 13.2 - - - +
65F HIS* 3.0 33.5 + - + +
68F LEU* 1.3 81.9 - - + +
70F PHE* 1.3 88.1 + - + +
156F ASP* 5.4 1.0 - - - +
160F LYS* 5.6 2.0 - - - -
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Residues in contact with PHE 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D LYS* 3.5 20.5 + - - +
334D LYS* 4.4 23.6 - - - -
65F HIS* 3.9 8.7 - + - -
66F VAL* 3.1 30.8 + - + +
67F ALA 3.7 2.3 - - - +
69F GLN* 1.3 97.7 - - + +
71F GLU* 1.3 64.2 + - - +
72F PRO* 3.6 4.9 - - - +
152F ARG* 5.1 4.3 - - + -
153F GLN* 3.7 38.8 - - + +
156F ASP* 3.3 43.5 - - + -
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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