Contacts of the helix formed by residues 74 - 89 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LYS* 1.3 90.6 - - + +
75A ASN* 1.3 59.8 + - - +
76A ARG* 2.8 9.2 + - - +
77A GLU* 2.7 67.2 + - - +
78A LYS* 3.0 16.5 + - - +
139A GLU* 3.3 13.2 - - - -
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Residues in contact with ASN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LYS 4.1 0.8 + - - -
74A THR* 1.3 70.3 - - - +
76A ARG* 1.3 57.0 + - - +
78A LYS* 3.7 21.0 - - - +
79A PHE 3.7 0.9 + - - -
130A ILE* 3.1 32.9 + - - +
133A GLU* 2.7 38.9 + - - +
134A GLY* 2.5 39.2 + - - -
137A ASN* 4.5 3.2 + - - +
139A GLU* 2.8 25.0 + - - +
140A TRP* 3.3 8.5 - - + -
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Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A THR* 2.8 12.5 + - - +
75A ASN* 1.3 75.3 - - - +
77A GLU* 1.3 72.8 + - - +
78A LYS 3.0 1.8 - - - -
79A PHE* 2.9 15.7 + - - +
80A TYR* 3.0 42.3 + - + +
139A GLU* 3.1 11.1 + - + +
140A TRP* 3.6 20.8 - - + -
183A LEU* 3.5 29.5 + - + +
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Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LYS 4.4 0.9 - - - +
72A ALA* 3.5 13.3 - - + +
73A LYS* 2.5 62.0 + - - +
74A THR* 2.7 35.7 + - - +
76A ARG* 1.3 81.4 + - - +
78A LYS* 1.3 57.4 + - - +
80A TYR* 3.3 10.7 + - + +
81A LEU* 2.9 30.0 + - - +
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Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TRP* 3.8 10.7 - - + -
69A GLN* 2.8 57.2 + - - +
70A ILE* 5.0 0.2 - - - +
72A ALA* 3.7 19.0 + - + -
73A LYS 5.4 2.0 - - - -
74A THR 3.0 16.4 + - - +
75A ASN* 3.7 24.2 - - - +
76A ARG 3.0 1.0 - - - -
77A GLU* 1.3 76.2 - - - +
79A PHE* 1.3 56.5 + - - +
81A LEU* 2.9 2.7 + - - +
82A TYR* 2.7 36.3 + - - +
129A VAL* 6.3 0.2 - - + -
130A ILE* 3.4 31.0 - - + -
133A GLU* 4.4 8.7 - - - +
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Residues in contact with PHE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASN 4.3 7.0 - - - +
76A ARG* 2.9 10.1 + - - +
78A LYS* 1.3 78.7 - - - +
80A TYR* 1.3 62.9 + - - +
82A TYR* 4.7 4.0 - - - -
83A ASN* 3.3 48.7 + - - +
127A TYR* 3.6 34.3 - + - -
130A ILE* 3.6 12.8 - - + +
131A PHE* 3.7 25.6 - + - -
140A TRP* 5.0 2.5 - - + -
152A ALA* 4.0 5.2 - - + -
156A VAL* 5.2 0.4 - - + -
178A PHE* 4.6 4.3 - + - -
179A SER* 3.8 18.4 - - - -
182A PHE* 3.3 27.8 - + + -
183A LEU* 3.4 37.5 - - + -
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Residues in contact with TYR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ARG* 3.0 44.6 + - + +
77A GLU* 3.6 11.9 - - + +
79A PHE* 1.3 76.5 - - - +
81A LEU* 1.3 62.4 + - - +
83A ASN* 3.9 2.6 - - - +
84A GLU* 3.3 20.5 + - - +
176A ASN* 3.6 42.6 + - + -
179A SER* 3.7 12.5 + - - -
180A GLN* 2.9 38.4 + - - +
183A LEU* 3.3 33.4 - - + -
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TRP* 3.4 25.1 - - + -
68A GLU* 3.7 36.3 - - - +
69A GLN* 4.1 3.8 - - - -
71A LYS* 6.0 0.9 - - + -
72A ALA* 4.6 9.6 - - + +
77A GLU 2.9 18.5 + - - +
78A LYS* 2.9 3.7 + - - +
80A TYR* 1.3 71.7 - - - +
82A TYR* 1.3 58.3 + - - +
83A ASN 3.0 1.3 - - - -
84A GLU* 2.6 37.6 + - + +
85A LEU* 2.8 34.0 + - + -
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Residues in contact with TYR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TRP* 3.2 34.0 + + - -
65A TRP* 3.6 42.1 - + + -
78A LYS 2.7 20.5 + - - +
79A PHE* 4.3 4.0 - - - +
81A LEU* 1.3 72.6 - - - +
83A ASN* 1.3 59.2 + - - +
85A LEU* 3.6 5.7 + - - +
86A SER* 3.3 21.0 + - - -
93A TYR* 4.7 4.7 - + - -
123A TYR* 3.3 31.2 - + - -
126A ALA* 3.1 30.3 - - + +
127A TYR* 3.1 55.9 - + - -
130A ILE* 5.5 4.9 - - + -
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Residues in contact with ASN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PHE* 3.3 40.8 + - - +
80A TYR 3.9 1.6 - - - +
81A LEU 3.0 1.0 - - - -
82A TYR* 1.3 75.8 - - - +
84A GLU* 1.3 65.1 + - - +
86A SER* 3.2 21.6 - - - -
87A LEU 4.0 1.2 + - - -
127A TYR* 2.5 36.2 + - - -
156A VAL* 3.4 16.7 - - - +
175A MET* 3.5 23.9 - - + +
178A PHE* 4.2 4.9 - - - -
179A SER* 3.1 26.0 + - - +
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR 3.3 12.7 + - - +
81A LEU* 2.6 24.9 + - + +
83A ASN* 1.3 71.7 - - - +
85A LEU* 1.3 73.3 + - - +
87A LEU* 3.0 18.0 + - - +
88A THR* 3.3 29.2 + - - +
172A ILE* 2.9 46.8 - - + +
175A MET* 4.5 6.7 - - - +
176A ASN* 4.2 8.5 - - - +
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TRP* 3.3 36.6 - - + -
64A GLN* 4.4 15.7 - - + +
65A TRP* 4.0 19.1 - - + -
68A GLU* 4.0 25.6 - - + +
81A LEU* 2.8 38.8 + - + +
82A TYR 3.7 6.7 - - - +
83A ASN 3.3 0.2 - - - -
84A GLU* 1.3 83.4 - - - +
86A SER* 1.3 59.4 + - - +
87A LEU 2.7 1.2 + - - -
88A THR* 2.7 10.8 + - - +
89A THR* 2.6 36.3 + - - +
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Residues in contact with SER 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TRP* 4.6 0.8 - - - -
82A TYR* 3.3 14.1 + - - -
83A ASN* 3.2 14.5 + - - -
85A LEU* 1.3 77.7 - - - +
87A LEU* 1.3 60.1 + - - +
89A THR* 4.0 4.2 + - - +
93A TYR* 3.5 56.0 + - - +
94A PRO* 5.6 0.5 - - - +
127A TYR* 4.7 1.4 + - - -
156A VAL* 3.8 8.7 - - - +
160A VAL* 3.8 28.2 - - - +
175A MET* 4.3 1.8 - - - -
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ASN 4.4 6.5 - - - +
84A GLU* 3.0 9.1 + - - +
85A LEU 2.7 4.2 + - - -
86A SER* 1.3 75.9 - - - +
88A THR* 1.3 64.5 + - + +
89A THR 3.4 4.0 - - - +
159A ILE* 5.2 3.8 - - + +
160A VAL* 3.6 39.5 - - + -
168A ILE* 5.6 7.3 - - + +
171A ARG* 3.3 63.2 + - + +
172A ILE* 3.5 12.3 - - + +
175A MET* 3.9 15.5 - - + -
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Residues in contact with THR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLU* 3.3 26.8 + - - +
85A LEU* 2.7 32.1 + - - +
87A LEU* 1.3 74.8 - - + +
89A THR* 1.3 65.6 + - - +
90A GLU* 5.0 1.9 - - - +
168A ILE* 6.3 3.6 - - + -
172A ILE* 5.1 5.4 - - + -
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Residues in contact with THR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TRP* 2.8 34.7 - - + -
64A GLN* 3.2 30.1 + - - +
85A LEU* 2.6 31.8 + - - +
86A SER* 4.0 8.0 + - - +
87A LEU 3.4 6.2 - - - +
88A THR* 1.3 78.6 + - - +
90A GLU* 1.3 72.3 + - - +
91A TYR* 3.0 26.2 - - + +
93A TYR* 5.2 2.5 - - - -
94A PRO* 3.8 13.3 - - - +
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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