Contacts of the helix formed by residues 68 - 78 (chain D) in PDB entry 3J41
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 ASN 68 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D TYR* 5.3 0.8 + - - -
66D HIS 2.6 14.4 + - - +
67D VAL* 1.3 79.2 - - - +
69D PRO* 1.3 70.6 - - - +
70D ALA* 2.8 23.5 + - - +
71D VAL* 2.9 27.8 + - + +
72D THR* 2.8 22.2 + - - -
93D GLN* 3.3 7.7 - - - -
138D THR* 5.6 0.2 - - - +
141D PHE* 3.9 10.8 - - + -
168D LEU* 6.1 0.2 - - - +
183D MET 2.6 27.1 + - - -
184D ASN* 3.3 17.4 - - - +
185D PRO* 3.4 5.5 - - - +
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Residues in contact with PRO 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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68D ASN* 1.3 83.9 - - - +
70D ALA* 1.3 51.4 - - - +
72D THR* 3.1 2.3 + - - -
73D PHE* 2.7 37.1 + - - +
90D MET* 3.5 35.6 - - + +
93D GLN* 3.2 23.6 - - + +
94D LEU* 4.5 9.4 - - + -
184D ASN* 3.4 17.0 - - - +
185D PRO* 4.1 14.1 - - + -
186D ALA* 3.4 25.8 - - + +
205D TRP* 4.6 2.0 - - + -
209D VAL* 5.8 1.3 - - + -
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Residues in contact with ALA 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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68D ASN* 2.8 18.8 + - - +
69D PRO* 1.3 75.3 - - - +
71D VAL* 1.3 56.3 + - - +
73D PHE* 3.5 6.8 - - - +
74D ALA 2.9 22.0 + - - -
138D THR* 4.3 5.4 - - + -
185D PRO* 3.7 7.9 - - + +
208D PRO* 3.6 43.5 - - + +
209D VAL* 4.1 5.8 - - - +
212D ALA* 3.0 17.6 - - + +
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Residues in contact with VAL 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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65D ALA 5.3 1.3 - - - +
66D HIS* 4.1 18.6 - - - +
68D ASN* 2.9 37.2 + - + +
70D ALA* 1.3 74.5 - - + +
72D THR* 1.3 65.8 + - - +
74D ALA* 3.1 10.6 + - + +
75D PHE* 3.0 44.7 + - + -
138D THR* 5.9 0.2 - - + -
141D PHE* 3.8 11.0 - - + -
142D VAL* 4.6 6.7 - - + -
145D ILE* 3.7 33.0 - - + -
146D PHE* 6.1 0.2 - - + -
149D TYR* 6.2 0.2 - - - +
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Residues in contact with THR 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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66D HIS* 2.9 24.7 - - - +
68D ASN 2.8 7.8 + - - -
69D PRO 3.5 7.6 - - - -
71D VAL* 1.3 72.3 - - - +
73D PHE* 1.3 68.3 + - - +
75D PHE 3.0 2.3 + - - -
76D LEU* 2.9 18.9 + - - +
81D MET* 3.5 13.8 - - + +
86D ALA* 3.5 44.0 - - + +
89D TYR* 3.7 2.3 - - + -
90D MET* 4.0 8.5 - - + -
93D GLN* 2.9 24.9 + - - -
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Residues in contact with PHE 73 (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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69D PRO 2.7 20.5 + - - +
70D ALA* 3.5 9.2 - - - +
72D THR* 1.3 74.8 - - - +
74D ALA* 1.3 67.7 + - - +
76D LEU* 3.0 28.3 + - + +
77D VAL* 3.1 40.3 + - + +
86D ALA* 6.0 0.2 - - - -
90D MET* 5.2 8.3 - - + -
209D VAL* 3.6 47.1 - - + -
212D ALA* 4.5 0.2 - - + -
213D GLY* 4.1 13.5 - - - -
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Residues in contact with ALA 74 (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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70D ALA 2.9 14.7 + - - +
71D VAL* 3.1 13.9 - - + +
73D PHE* 1.3 79.9 - - - +
75D PHE* 1.3 57.8 + - - +
77D VAL* 3.3 5.1 - - - +
78D GLY 3.1 11.4 + - - -
142D VAL* 3.8 20.2 - - + -
146D PHE* 3.3 10.3 - - + -
212D ALA* 3.7 25.1 - - + +
216D SER* 3.0 21.8 + - - -
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Residues in contact with PHE 75 (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 HIS* 3.2 34.5 - + - +
71D VAL* 3.0 36.3 + - + -
72D THR 3.0 7.2 + - - +
74D ALA* 1.3 75.3 - - - +
76D LEU* 1.3 62.5 + - - +
78D GLY* 3.5 1.1 + - - -
79D SER 3.3 2.1 + - - -
80D GLN* 2.9 63.1 + - + +
81D MET* 3.7 16.9 + - + -
145D ILE* 3.5 25.6 - - + -
146D PHE* 3.7 26.0 - + - -
149D TYR* 3.5 25.1 - + + -
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Residues in contact with LEU 76 (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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72D THR 2.9 11.1 + - - +
73D PHE* 3.0 25.1 + - + +
75D PHE* 1.3 74.4 - - - +
77D VAL* 1.3 58.0 + - + +
78D GLY 2.8 4.0 - - - -
79D SER* 2.6 28.9 + - - -
81D MET* 3.7 23.0 - - + +
82D SER 3.8 4.5 - - - +
83D LEU* 3.8 44.6 - - + +
86D ALA* 3.9 15.7 - - + -
42F ASN 5.5 1.0 - - - +
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Residues in contact with VAL 77 (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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73D PHE* 3.1 48.7 + - + +
74D ALA* 3.3 15.5 - - - +
76D LEU* 1.3 78.3 - - + +
78D GLY* 1.3 60.8 + - - +
79D SER* 3.1 6.7 + - - -
213D GLY* 4.7 3.8 - - - -
216D SER* 3.5 17.1 + - - +
217D LEU* 4.6 15.9 - - + +
220D ASP* 4.4 2.6 - - - +
221D PHE* 4.5 9.2 - - - -
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Residues in contact with GLY 78 (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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74D ALA 3.1 11.2 + - - -
75D PHE 3.5 2.7 + - - -
76D LEU 2.8 1.6 - - - -
77D VAL* 1.3 77.4 - - - +
79D SER* 1.3 70.6 + - - +
80D GLN* 3.4 12.9 + - - +
146D PHE* 4.6 5.2 - - - -
216D SER* 3.5 10.1 - - - -
220D ASP* 3.4 24.5 - - - +
221D PHE* 4.8 4.2 - - - -
222D LEU* 5.7 3.1 + - - +
44F THR* 4.9 1.2 - - - +
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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