Contacts of the helix formed by residues 88 - 106 (chain Q) in PDB entry 3J7Y
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 ASP 88 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E LEU* 3.9 28.7 + - + +
123E GLN* 5.3 0.9 - - - +
125E GLN* 4.8 10.0 + - - -
150E LYS* 5.5 5.5 + - - -
294E ASN* 3.1 29.9 + - - +
87Q THR* 1.3 76.6 + - - +
89Q PRO* 1.3 73.0 - - + +
90Q LEU* 3.3 11.2 + - + +
91Q LYS* 3.5 17.4 + - + +
92Q PHE* 3.8 4.9 - - - -
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Residues in contact with PRO 89 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87Q THR 3.5 2.9 - - - +
88Q ASP* 1.3 87.8 - - + +
90Q LEU* 1.3 59.5 + - + +
91Q LYS 3.2 0.2 - - - -
92Q PHE* 3.2 17.8 + - + +
93Q GLN* 2.9 39.6 + - + +
96Q ARG* 5.1 1.4 + - - +
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Residues in contact with LEU 90 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E LEU* 4.3 2.9 - - + -
123E GLN* 3.2 33.0 - - - +
280E HIS* 3.6 29.8 - - + +
282E ILE* 4.1 4.5 - - + -
88Q ASP* 3.2 10.7 - - + +
89Q PRO* 1.3 80.4 - - + +
91Q LYS* 1.3 56.8 + - - +
93Q GLN* 3.2 15.3 + - + +
94Q ILE* 2.9 58.6 + - + +
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Residues in contact with LYS 91 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3150A U 5.0 3.8 - - - -
104E LEU* 4.3 21.6 - - + +
105E GLY* 3.8 11.7 - - - -
106E MET 3.1 43.0 + - - +
107E MET* 4.3 1.1 - - - -
121E LEU* 3.7 22.2 - - + -
87Q THR* 4.3 14.0 + - - +
88Q ASP* 3.5 11.3 + - - +
89Q PRO 3.2 0.2 - - - -
90Q LEU* 1.3 79.1 - - - +
92Q PHE* 1.3 65.4 + - + +
94Q ILE* 3.2 12.6 + - - +
95Q GLU* 2.7 56.0 + - + +
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Residues in contact with PHE 92 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80Q PHE 5.7 0.9 - - - -
82Q PRO* 3.3 41.1 - - + -
83Q ARG* 4.4 12.8 - - + -
85Q GLY 5.3 1.8 - - - -
87Q THR* 3.5 39.9 - - + -
88Q ASP 3.8 14.4 - - - -
89Q PRO* 3.2 16.7 + - + +
91Q LYS* 1.3 83.4 - - + +
93Q GLN* 1.3 57.7 + - - +
95Q GLU* 3.2 22.4 + - + +
96Q ARG* 2.9 47.0 + - + +
143Q ARG* 5.9 6.1 - - + -
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Residues in contact with GLN 93 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280E HIS* 5.6 8.1 - - + -
89Q PRO* 2.9 26.1 + - + +
90Q LEU* 3.3 15.4 - - + +
92Q PHE* 1.3 76.3 - - - +
94Q ILE* 1.3 57.0 + - + +
96Q ARG* 3.2 17.7 + - - +
97Q LYS* 2.9 30.2 + - - +
285Q GLU* 3.4 25.8 + - - +
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Residues in contact with ILE 94 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E LEU* 5.0 0.2 - - + -
107E MET* 4.5 8.3 - - + -
121E LEU* 4.3 18.4 - - + -
275E ARG* 5.8 0.2 - - - +
277E ASN* 4.6 11.4 - - - +
280E HIS* 4.7 9.6 - - + +
282E ILE* 3.7 25.4 - - + -
284E TYR* 3.2 25.1 - - + +
90Q LEU* 2.9 41.6 + - + +
91Q LYS* 3.3 9.6 - - - +
93Q GLN* 1.3 76.9 - - + +
95Q GLU* 1.3 63.8 + - - +
97Q LYS* 3.3 8.4 + - - +
98Q ASP* 3.2 26.5 + - - +
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Residues in contact with GLU 95 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3150A U 5.4 3.3 + - - +
106E MET 4.8 0.8 - - - +
107E MET* 3.9 32.6 - - - +
108E PRO* 5.2 0.3 - - - +
91Q LYS* 2.7 43.4 + - + +
92Q PHE* 3.2 27.4 + - + +
94Q ILE* 1.3 77.0 - - - +
96Q ARG* 1.3 58.6 + - + +
98Q ASP* 3.3 8.5 + - - +
99Q MET* 3.0 33.3 + - - +
143Q ARG* 4.1 5.9 - - - +
144Q GLY* 3.5 27.7 - - - -
145Q LEU* 3.6 10.8 + - + +
146Q GLY 4.7 1.0 + - - -
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Residues in contact with ARG 96 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80Q PHE* 3.8 33.2 + - + +
82Q PRO* 6.0 1.2 - - - +
89Q PRO* 5.1 1.4 + - - +
92Q PHE* 2.9 23.8 + - + +
93Q GLN* 3.2 28.5 + - - +
95Q GLU* 1.3 73.9 - - + +
97Q LYS* 1.3 59.2 + - - +
99Q MET* 3.2 23.0 + - + +
100Q LEU* 2.8 41.7 + - + +
281Q ALA* 6.0 0.4 - - - +
282Q ILE* 3.7 26.1 - - - +
285Q GLU* 3.0 49.4 + - - +
286Q ILE* 6.2 0.7 - - - -
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Residues in contact with LYS 97 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E LYS* 3.8 26.3 - - - +
280E HIS* 5.7 5.6 + - - +
330E GLU* 6.0 3.2 - - - +
93Q GLN 2.9 13.2 + - - +
94Q ILE* 3.6 11.9 - - - +
95Q GLU 3.3 0.4 - - - -
96Q ARG* 1.3 75.7 - - - +
98Q ASP* 1.3 61.1 + - - +
100Q LEU* 3.2 14.9 + - + +
101Q GLU* 2.9 28.6 + - - +
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Residues in contact with ASP 98 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E MET* 4.0 3.7 - - - +
275E ARG* 3.1 33.6 + - - -
340E PRO* 3.5 33.0 - - + +
94Q ILE* 3.2 13.1 + - - +
95Q GLU* 3.5 9.9 - - - +
97Q LYS* 1.3 81.3 - - - +
99Q MET* 1.3 58.8 + - - +
101Q GLU* 3.2 4.7 + - - +
102Q ARG* 2.9 28.6 + - - +
145Q LEU* 3.8 29.7 - - + +
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Residues in contact with MET 99 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79Q GLU* 3.8 14.4 - - - +
80Q PHE* 3.6 41.1 - - + -
95Q GLU 3.0 14.0 + - - +
96Q ARG* 3.3 24.9 - - + +
98Q ASP* 1.3 76.8 - - - +
100Q LEU* 1.3 56.6 + - - +
102Q ARG* 3.2 4.2 + - - +
103Q ARG* 2.9 34.5 + - - +
144Q GLY* 3.2 40.8 - - - +
145Q LEU* 3.9 4.2 - - + +
167Q TYR* 3.4 40.5 - - + +
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Residues in contact with LEU 100 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80Q PHE* 4.2 15.0 - - + -
96Q ARG* 2.8 28.9 + - + +
97Q LYS* 3.2 14.1 + - + +
99Q MET* 1.3 76.9 - - - +
101Q GLU* 1.3 62.7 + - - +
103Q ARG* 3.2 20.1 + - + +
104Q LYS* 3.2 19.6 + - - +
285Q GLU* 4.9 6.3 - - + +
286Q ILE* 4.1 30.7 - - + -
289Q SER* 3.6 37.0 - - - +
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Residues in contact with GLU 101 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340E PRO* 3.4 35.2 - - + +
341E GLY* 3.6 8.3 - - - +
97Q LYS* 2.9 13.6 + - + +
98Q ASP* 3.4 9.9 - - - +
100Q LEU* 1.3 75.5 - - - +
102Q ARG* 1.3 64.4 + - - +
104Q LYS* 2.9 56.2 + - - +
105Q VAL* 3.7 7.4 + - - +
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Residues in contact with ARG 102 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339E GLN 5.7 1.3 + - - -
340E PRO* 4.7 12.3 - - + +
341E GLY 4.6 5.1 - - - +
342E ALA 4.7 5.9 + - - -
344E SER* 3.6 25.3 - - - +
98Q ASP 2.9 12.9 + - - +
99Q MET 3.2 8.9 + - - +
101Q GLU* 1.3 76.5 - - - +
103Q ARG* 1.3 56.5 + - - +
105Q VAL* 2.9 36.3 + - - +
106Q LEU* 3.1 56.5 + - + +
108Q ILE* 5.1 1.3 - - + -
145Q LEU* 5.5 2.7 - - + -
166Q LEU 4.4 0.2 + - - -
167Q TYR* 3.8 35.7 + - + -
168Q ASN 2.7 29.4 + - - -
169Q PRO* 3.9 10.8 + - - +
170Q ARG 4.0 0.4 + - - -
171Q VAL 4.4 0.4 + - - -
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Residues in contact with ARG 103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75Q PHE* 5.4 5.5 - - - -
77Q SER* 3.1 35.8 + - - -
79Q GLU* 4.6 3.0 - - - +
80Q PHE* 3.7 16.6 - - - -
99Q MET 2.9 21.0 + - - +
100Q LEU* 3.2 14.1 + - + +
102Q ARG* 1.3 76.2 - - - +
104Q LYS* 1.3 52.8 + - - +
106Q LEU 2.7 28.4 - - - +
107Q HIS* 4.2 10.8 - - - +
108Q ILE* 3.3 54.3 + - + +
140Q ARG* 5.2 0.4 - - - +
166Q LEU* 4.8 1.4 - - - +
167Q TYR* 2.9 27.4 + - + -
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Residues in contact with LYS 104 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341E GLY* 6.1 0.9 - - - -
100Q LEU* 3.2 17.0 + - - +
101Q GLU* 2.9 40.8 + - - +
103Q ARG* 1.3 76.1 - - - +
105Q VAL* 1.3 62.9 + - + +
106Q LEU 3.4 4.3 - - - +
289Q SER* 5.2 11.0 + - - -
292Q SER* 5.0 11.3 + - - -
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Residues in contact with VAL 105 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341E GLY* 3.1 38.8 - - - +
342E ALA 3.5 16.8 - - - +
343E PRO* 3.9 5.8 - - + -
344E SER* 3.9 13.2 - - - +
101Q GLU 4.2 2.0 - - - +
102Q ARG* 2.9 34.1 + - - +
104Q LYS* 1.3 78.4 - - + +
106Q LEU* 1.3 64.7 + - + +
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Residues in contact with LEU 106 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344E SER* 4.4 4.3 - - - +
102Q ARG* 3.1 51.8 + - + +
103Q ARG 2.7 19.7 - - - +
104Q LYS 3.4 4.7 - - - +
105Q VAL* 1.3 85.8 - - + +
107Q HIS* 1.3 60.5 + - - +
108Q ILE* 4.0 28.7 - - + +
166Q LEU 4.1 10.3 - - - +
171Q VAL* 3.6 24.7 - - + +
172Q GLN 3.3 26.0 - - - +
173Q GLU* 6.0 1.8 - - - -
174Q ILE* 5.5 2.0 - - + -
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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