Contacts of the helix formed by residues 60 - 72 (chain D) 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 GLY 60 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59D SER* 1.3 75.0 - - - +
61D LYS* 1.3 68.2 + - - +
62D SER 3.2 4.4 + - - -
63D THR* 3.2 11.8 + - - -
64D PHE* 3.3 14.2 + - - +
246D CYS* 4.6 6.4 - - - -
291D ASN* 3.6 12.8 - - - -
348D ALA* 4.3 3.3 - - - +
476D GDP 2.9 32.0 + - - -
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Residues in contact with LYS 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LEU* 3.6 28.0 - - + +
54D LEU* 3.3 39.0 - - - +
55D GLY 3.0 28.3 - - - -
56D ALA 3.8 0.2 - - - -
59D SER* 3.8 1.3 - - - -
60D GLY* 1.3 76.8 - - - +
62D SER* 1.3 60.6 + - - +
64D PHE* 3.9 2.4 + - - +
65D LEU* 3.6 13.2 + - - +
222D ASP* 3.3 14.8 - - - +
223D VAL* 2.7 25.6 + - + +
224D GLY 4.4 1.1 - - - -
225D GLY* 3.4 4.0 - - - +
246D CYS* 4.2 19.0 - - + -
378D ALF 2.9 33.2 - - - -
476D GDP 3.1 16.6 + - - +
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Residues in contact with SER 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D LYS* 1.3 71.9 - - - +
63D THR* 1.3 68.5 + - - +
64D PHE 3.1 1.8 - - - -
65D LEU* 3.0 6.6 + - - +
66D LYS* 2.9 37.9 + - - +
201D ARG 5.5 2.2 - - - -
203D THR* 3.3 5.6 + - - -
222D ASP* 2.7 22.5 + - - -
377D MG 2.3 29.1 - - - -
476D GDP 2.9 14.4 + - - -
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Residues in contact with THR 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D GLY 3.2 6.7 + - - -
62D SER* 1.3 76.4 - - - +
64D PHE* 1.3 63.4 + - - +
66D LYS* 3.2 15.0 + - - +
67D GLN* 3.1 23.3 + - - +
197D LEU* 3.5 26.4 + - + +
348D ALA* 3.5 34.1 - - + +
349D THR* 4.0 11.2 - - + -
476D GDP 3.1 39.4 + - + -
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Residues in contact with PHE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LEU* 3.7 28.7 - - + -
60D GLY 3.3 10.8 + - - +
61D LYS* 3.9 5.4 - - - +
62D SER 3.1 0.6 - - - -
63D THR* 1.3 77.9 - - - +
65D LEU* 1.3 62.2 + - - +
67D GLN* 2.9 23.8 + - - +
68D MET* 3.0 29.7 + - + +
220D MET* 3.7 25.1 - - + -
244D ILE* 4.2 11.4 - - + -
246D CYS* 5.6 4.3 - - - -
289D PHE* 4.1 23.3 - + - -
348D ALA* 4.3 8.4 - - + +
354D VAL* 3.7 25.8 - - + -
357D VAL* 5.6 0.4 - - + -
358D PHE* 3.4 33.0 - + + -
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Residues in contact with LEU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LEU* 4.2 5.8 - - + -
61D LYS 3.6 10.5 + - - +
62D SER* 3.0 10.1 + - - +
64D PHE* 1.3 83.5 - - - +
66D LYS* 1.3 60.8 + - + +
68D MET* 3.2 6.6 + - + +
69D ARG* 3.2 20.8 + - - +
207D HIS* 4.9 8.5 - - + +
209D THR* 3.2 41.1 - - + +
220D MET* 3.4 28.7 - - + -
222D ASP* 3.9 26.7 - - + +
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Residues in contact with LYS 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D SER* 2.9 29.8 + - - +
63D THR* 3.3 14.4 - - - +
64D PHE 3.1 0.2 - - - -
65D LEU* 1.3 76.4 - - + +
67D GLN* 1.3 57.3 + - - +
69D ARG* 3.5 2.4 + - - -
70D ILE* 3.0 32.0 + - - +
76D PHE* 3.5 22.4 - - + -
84D PHE* 3.6 22.1 - - - -
196D ILE* 3.0 35.8 + - + +
197D LEU* 4.2 11.1 + - + -
199D ALA 3.1 22.0 + - - -
201D ARG* 5.2 8.8 - - - +
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Residues in contact with GLN 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D THR 3.1 14.8 + - - +
64D PHE* 2.9 14.2 + - - +
66D LYS* 1.3 76.8 - - - +
68D MET* 1.3 66.4 + - + +
69D ARG 3.1 0.2 - - - -
70D ILE* 3.9 10.8 - - - +
71D ILE* 2.5 42.0 + - + +
197D LEU* 3.5 23.8 - - + +
348D ALA 2.7 26.5 + - - +
349D THR 3.8 0.8 - - - -
350D ASP 3.9 1.2 + - - -
351D THR* 3.3 45.8 + - - +
354D VAL* 3.8 12.8 - - + +
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Residues in contact with MET 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D PHE* 3.0 38.4 + - + +
65D LEU* 3.2 11.2 + - + +
67D GLN* 1.3 79.4 - - - +
69D ARG* 1.3 58.4 + - - +
71D ILE* 4.1 6.5 - - + -
72D HIS* 2.9 23.9 + - - +
73D GLY 2.7 21.1 + - - -
209D THR* 6.1 0.7 - - + -
211D PHE* 4.1 21.6 - - + -
220D MET* 3.8 17.3 - - + -
354D VAL* 3.5 32.5 - - + -
358D PHE* 3.8 36.1 - - + -
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Residues in contact with ARG 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D LEU 3.2 12.2 + - - +
66D LYS* 3.6 9.0 - - - +
67D GLN 3.1 0.4 - - - -
68D MET* 1.3 77.8 - - - +
70D ILE* 1.3 62.5 + - - +
73D GLY* 3.1 15.8 + - - +
74D GLN* 3.4 30.9 + - - +
75D ASP* 2.8 50.9 + - - +
76D PHE* 3.3 42.6 - - + +
77D ASP* 4.8 4.0 + - - -
80D ALA* 4.4 12.5 - - - +
209D THR* 5.9 7.8 - - + +
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Residues in contact with ILE 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D LYS 3.0 24.4 + - - +
67D GLN* 3.0 23.5 + - - +
69D ARG* 1.3 80.9 - - - +
71D ILE* 1.3 68.9 + - + +
73D GLY 4.5 1.9 - - - +
75D ASP* 3.1 28.9 - - - +
76D PHE* 3.6 13.2 - - + -
193D GLN* 3.3 28.5 - - + +
196D ILE* 6.0 0.7 - - + -
197D LEU* 4.2 22.4 - - + -
351D THR* 4.8 10.3 - - + +
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Residues in contact with ILE 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D GLN* 2.5 26.4 + - + +
68D MET* 4.1 5.6 - - + -
70D ILE* 1.3 78.7 - - + +
72D HIS* 1.3 88.3 + - + +
73D GLY 4.8 0.6 - - - +
351D THR* 4.3 22.4 - - + +
354D VAL* 3.9 20.2 - - + -
355D GLN* 3.9 42.8 - - + +
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Residues in contact with HIS 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D MET* 2.9 26.4 + - + +
71D ILE* 1.3 97.0 - - + +
73D GLY* 1.3 69.4 + - - +
211D PHE* 4.1 21.8 - + + -
212D THR 4.2 10.7 - - - +
213D PHE* 3.3 35.2 - + + -
355D GLN* 6.0 2.0 - - + +
358D PHE* 3.3 41.8 - + + -
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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