Contacts of the helix formed by residues 74 - 89 (chain D) in PDB entry 1JT0
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 THR 74 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D LYS* 1.3 80.1 - - + +
75D ASN* 1.3 55.7 + - - +
76D ARG* 3.3 5.5 + - - +
77D GLU* 3.0 39.5 + - - +
78D LYS* 3.0 31.0 + - - +
137D ASN* 6.2 1.6 - - - +
139D GLU* 2.8 24.2 + - + +
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Residues in contact with ASN 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D THR* 1.3 70.5 - - - +
76D ARG* 1.3 64.4 + - - +
78D LYS* 2.9 24.5 + - - +
79D PHE* 2.8 21.5 + - - +
129D VAL* 5.5 0.5 - - - +
130D ILE* 3.3 34.4 - - + +
133D GLU* 2.9 32.3 + - - +
134D GLY* 2.8 29.3 - - - +
137D ASN* 4.7 3.2 - - - +
139D GLU* 2.7 23.5 + - - +
140D TRP* 3.8 7.6 - - + -
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Residues in contact with ARG 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D THR* 3.5 8.5 - - - +
75D ASN* 1.3 80.2 - - - +
77D GLU* 1.3 64.3 + - + +
79D PHE* 3.1 10.4 + - - +
80D TYR* 3.3 29.2 + - + -
139D GLU* 3.0 19.6 + - + +
140D TRP* 3.7 31.7 - - + -
180D GLN* 5.5 0.8 + - - +
183D LEU* 3.3 40.5 + - + +
184D ASN* 4.6 14.1 + - - +
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Residues in contact with GLU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D LYS 4.2 2.3 - - - +
72D ALA* 3.8 12.7 - - + +
73D LYS* 3.1 32.9 + - - +
74D THR* 3.0 44.0 + - - +
76D ARG* 1.3 81.4 - - + +
78D LYS* 1.3 62.1 + - - +
80D TYR* 3.6 8.6 + - - +
81D LEU* 3.0 23.4 + - - +
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Residues in contact with LYS 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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65D TRP* 3.8 9.5 - - + -
69D GLN* 3.0 49.7 + - - +
72D ALA* 3.7 22.2 - - + -
73D LYS 4.5 4.5 - - - -
74D THR 3.0 21.0 + - - +
75D ASN* 2.9 33.8 + - - +
77D GLU* 1.3 76.6 - - - +
79D PHE* 1.3 53.0 + - - +
81D LEU* 2.9 4.9 + - - +
82D TYR* 2.6 35.5 + - - +
129D VAL* 6.5 0.9 - - + -
130D ILE* 4.0 20.4 - - + -
133D GLU* 4.6 9.2 - - - -
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Residues in contact with PHE 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ASN 2.8 13.9 + - - +
76D ARG 3.4 9.0 - - - +
78D LYS* 1.3 72.2 - - - +
80D TYR* 1.3 64.1 + - - +
82D TYR* 3.1 2.5 + - - +
83D ASN* 3.0 44.3 + - - -
127D TYR* 3.4 36.1 - + - -
130D ILE* 4.0 16.0 - - + +
131D PHE* 3.7 20.6 - + - -
140D TRP* 5.1 0.9 - - + -
152D ALA* 4.2 5.2 - - + -
156D VAL* 5.6 0.2 - - + -
178D PHE* 4.8 4.9 - + - -
179D SER* 3.8 18.4 - - - -
182D PHE* 3.5 28.5 - + + -
183D LEU* 3.3 42.0 - - + -
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Residues in contact with TYR 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ARG* 3.3 30.8 + - + -
77D GLU* 3.8 8.7 - - - +
79D PHE* 1.3 78.8 - - - +
81D LEU* 1.3 58.5 + - - +
83D ASN* 3.5 1.4 + - - +
84D GLU* 2.9 30.6 + - - +
176D ASN* 3.4 35.7 - - + +
179D SER* 3.8 22.7 - - - -
180D GLN* 3.2 29.5 - - + +
183D LEU* 3.4 26.5 - - + -
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Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D TRP* 3.8 19.5 - - + -
68D GLU* 3.3 35.7 - - + +
69D GLN* 4.1 4.7 - - - -
71D LYS* 5.6 2.9 - - + -
72D ALA* 4.6 10.3 - - + +
77D GLU 3.0 13.8 + - - +
78D LYS* 2.9 9.0 + - - +
80D TYR* 1.3 76.6 - - - +
82D TYR* 1.3 60.4 + - - +
84D GLU* 4.5 11.0 - - + -
85D LEU* 2.8 56.9 + - + +
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Residues in contact with TYR 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D TRP* 3.3 33.8 + + - -
62D GLN* 5.7 1.4 + - - -
65D TRP* 3.5 45.2 - + + -
78D LYS 2.6 18.4 + - - +
79D PHE* 3.1 5.1 + - - +
81D LEU* 1.3 72.5 - - - +
83D ASN* 1.3 63.2 + - - +
85D LEU* 3.3 2.7 + - - +
86D SER* 3.0 24.6 + - - -
93D TYR* 5.8 3.8 - + - -
122D LYS 4.5 1.0 + - - -
123D TYR* 3.2 33.0 - + - -
126D ALA* 3.5 25.0 - - + +
127D TYR* 3.5 46.9 - + + -
130D ILE* 4.2 9.0 - - + -
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Residues in contact with ASN 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D PHE* 3.0 40.0 + - - +
80D TYR 3.8 0.4 - - - +
82D TYR* 1.3 73.2 - - - +
84D GLU* 1.3 65.2 + - - +
85D LEU 3.0 1.6 - - - -
86D SER* 2.7 24.6 + - - -
87D LEU* 3.5 6.6 + - - +
127D TYR* 2.3 36.7 + - - -
156D VAL* 3.5 12.6 - - - +
175D MET* 3.8 23.5 - - + +
178D PHE* 4.8 0.6 - - - -
179D SER* 3.1 28.2 + - - +
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Residues in contact with GLU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D TYR 2.9 18.4 + - - +
81D LEU* 4.0 13.0 - - + +
83D ASN* 1.3 75.4 - - - +
85D LEU* 1.3 59.6 + - + +
87D LEU* 3.0 26.2 - - - +
88D THR* 3.1 20.0 + - + +
172D ILE* 3.7 31.2 - - + +
175D MET* 4.2 8.1 - - - +
176D ASN* 3.8 21.2 + - - +
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Residues in contact with LEU 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D TRP* 3.3 19.1 - - + -
64D GLN* 3.2 32.1 - - + +
65D TRP* 4.0 15.0 - - + -
68D GLU* 3.9 34.3 - - + +
81D LEU* 2.8 34.4 + - + +
82D TYR 3.5 5.8 - - - +
84D GLU* 1.3 77.2 - - + +
86D SER* 1.3 56.0 + - - +
87D LEU 2.8 5.2 - - - -
88D THR* 3.6 13.7 - - - +
89D THR* 2.6 38.5 + - - +
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Residues in contact with SER 86 (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 TRP* 4.4 5.4 - - - -
82D TYR* 3.0 14.7 + - - -
83D ASN* 2.7 21.0 + - - -
85D LEU* 1.3 74.4 - - - +
87D LEU* 1.3 58.1 + - - +
89D THR* 3.7 12.4 - - - +
93D TYR* 3.3 51.9 - - - +
127D TYR* 5.8 1.6 - - - -
156D VAL* 3.8 17.4 - - - +
160D VAL* 3.7 14.7 - - - +
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Residues in contact with LEU 87 (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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83D ASN 3.9 2.0 - - - +
84D GLU* 3.0 16.6 - - - +
86D SER* 1.3 82.6 + - - +
88D THR* 1.3 61.8 + - + +
89D THR 3.5 3.7 - - - +
159D ILE* 5.1 2.2 - - + +
160D VAL* 3.6 30.0 - - + +
168D ILE* 4.0 14.9 - - + +
171D ARG* 3.3 52.7 - - + +
172D ILE* 3.7 10.3 - - + -
175D MET* 3.4 36.3 - - + -
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Residues in contact with THR 88 (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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84D GLU* 3.1 23.4 + - + +
85D LEU* 3.5 19.8 + - - +
87D LEU* 1.3 78.0 - - - +
89D THR* 1.3 69.4 + - - +
90D GLU* 4.6 2.8 - - - +
168D ILE* 4.3 10.5 - - + -
172D ILE* 4.0 26.5 - - + -
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Residues in contact with THR 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D TRP* 3.3 32.0 - - + -
64D GLN* 3.3 16.1 + - - +
85D LEU 2.6 25.4 + - - +
86D SER* 3.7 20.6 - - - +
87D LEU 4.3 4.2 - - - +
88D THR* 1.3 79.7 + - - +
90D GLU* 1.3 66.0 + - - +
91D TYR* 3.1 22.3 + - - +
93D TYR* 4.0 11.0 - - + -
94D PRO* 3.6 9.9 - - + +
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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
------------------------------------------------------------
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