Contacts of the strand formed by residues 110 - 122 (chain Q) in PDB entry 1JJ2
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 110 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37Q GLY* 4.0 20.6 - - - +
38Q LYS 3.7 4.0 - - - -
39Q THR* 4.5 4.9 + - - +
108Q ALA 3.7 1.3 + - - -
109Q MET* 1.3 71.8 - - - +
111Q ILE* 1.3 75.4 + - - +
112Q LYS* 3.1 8.1 + - + +
147Q LEU* 3.2 5.1 - - - -
148Q GLU* 2.8 48.4 + - - +
149Q GLU 5.5 0.4 - - - -
150Q PRO* 4.5 15.5 - - - +
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Residues in contact with ILE 111 (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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35Q ILE* 3.5 31.6 - - + +
36Q LYS* 4.0 5.3 - - - +
37Q GLY* 3.0 22.0 + - - -
38Q LYS 2.8 20.6 + - - +
39Q THR 4.4 0.7 - - - +
40Q ALA* 4.4 4.5 - - - +
43Q ALA* 3.7 28.5 - - + -
92Q LEU* 4.0 9.0 - - + -
110Q THR* 1.3 70.9 - - - +
112Q LYS* 1.3 62.5 + - - +
113Q HIS 4.1 2.2 - - - +
114Q VAL* 3.8 22.7 - - + -
145Q LEU* 3.2 25.1 - - + -
146Q ILE 3.8 4.0 - - - -
147Q LEU* 4.0 17.0 - - + -
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Residues in contact with LYS 112 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6Q VAL* 4.5 11.1 - - + +
7Q GLU 3.4 24.0 + - - +
8Q ALA* 4.7 5.3 - - - +
9Q ASP 5.3 1.4 - - - +
13Q THR* 5.0 2.3 + - - +
36Q LYS* 3.5 21.7 + - - -
110Q THR* 3.1 9.1 + - - -
111Q ILE* 1.3 72.0 - - - +
113Q HIS* 1.3 64.7 + - + +
146Q ILE* 2.8 28.5 + - + +
148Q GLU* 3.9 45.6 + - + +
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Residues in contact with HIS 113 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5250 G 3.3 27.9 + - - -
5Q SER* 3.4 9.8 + - - -
6Q VAL* 3.5 27.1 - - + +
36Q LYS* 4.9 10.1 - - + +
111Q ILE* 3.4 1.1 - - - -
112Q LYS* 1.3 86.4 - - + +
114Q VAL* 1.3 68.7 + - - +
115Q ALA* 4.1 11.3 - - + +
144Q GLU* 3.1 46.5 + - + +
145Q LEU* 3.2 8.9 - - - +
146Q ILE* 2.8 53.1 + - + +
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Residues in contact with VAL 114 (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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5250 G 4.6 9.0 - - - +
32Q ALA* 3.4 43.7 - - + +
35Q ILE* 4.4 9.6 - - + -
36Q LYS* 3.6 30.2 - - + +
88Q PHE* 4.2 16.8 - - + -
91Q LEU* 5.0 1.6 - - + -
111Q ILE* 3.8 10.1 - - + -
113Q HIS* 1.3 80.1 - - - +
115Q ALA* 1.3 68.2 + - - +
143Q VAL* 4.5 3.4 - - + -
144Q GLU 3.2 11.4 - - - +
145Q LEU* 3.9 10.3 - - + -
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Residues in contact with ALA 115 (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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5240 A 3.5 16.4 - - - +
5250 G 3.9 17.7 - - - +
32Q ALA* 4.3 6.3 - - - -
113Q HIS* 4.1 6.1 - - - +
114Q VAL* 1.3 79.6 - - - +
116Q ALA* 1.3 60.1 + - - +
117Q HIS* 3.6 14.4 + - + -
143Q VAL* 3.2 7.2 - - - -
144Q GLU* 3.0 42.7 + - - +
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Residues in contact with ALA 116 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5240 A 2.7 33.2 + - - +
25Q PHE* 3.5 12.4 - - + -
28Q SER* 3.6 39.7 - - - +
29Q LYS* 4.4 4.6 - - + +
32Q ALA* 4.6 3.0 - - - +
88Q PHE* 5.0 1.1 - - + -
115Q ALA* 1.3 71.7 - - - +
117Q HIS* 1.3 67.6 + - - +
141Q VAL* 3.9 10.3 - - + -
142Q ASP 3.4 4.9 - - - +
143Q VAL* 4.2 7.4 - - + -
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Residues in contact with HIS 117 (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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200 G 3.2 36.7 + - - +
210 G 4.4 7.0 - - - +
5230 C 5.8 1.6 - - - +
5240 A 3.3 28.3 + - - -
2Q ILE* 3.7 38.6 - - + +
5Q SER* 4.7 1.8 + - - -
25Q PHE* 3.5 6.7 - - - -
115Q ALA* 3.6 24.3 + - + -
116Q ALA* 1.3 75.1 - - - +
118Q LYS* 1.3 62.1 + - - +
119Q VAL* 3.3 1.1 + - + +
141Q VAL* 3.5 2.9 - - - -
142Q ASP 2.9 32.5 + - - +
144Q GLU* 3.1 30.3 + - + -
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Residues in contact with LYS 118 (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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210 G 3.9 17.5 + - - +
220 U 4.2 8.5 - - - +
5230 C 5.1 4.1 + - - +
13660 C 4.9 14.9 + - - +
25Q PHE* 3.3 35.9 - - + -
117Q HIS* 1.3 71.9 - - - +
119Q VAL* 1.3 59.9 + - - +
120Q GLY* 3.8 15.5 - - - +
121Q GLU* 3.3 40.9 + - - -
139Q PRO* 4.0 15.7 - - - +
140Q GLN 3.6 6.7 - - - +
8506Q CL 3.3 29.1 - - + +
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Residues in contact with VAL 119 (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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210 G 4.0 11.4 - - - +
220 U 3.4 42.6 - - - +
230 G 4.9 1.9 + - - -
1Q GLY* 4.1 11.4 - - - +
2Q ILE* 4.4 4.0 - - + -
20Q GLU* 4.9 15.3 - - + +
117Q HIS 3.7 5.2 - - - +
118Q LYS* 1.3 73.7 - - - +
120Q GLY* 1.3 55.7 + - - +
140Q GLN* 2.8 17.5 + - + +
142Q ASP* 3.3 44.2 - - + +
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Residues in contact with GLY 120 (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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220 U 5.0 5.6 - - - -
230 G 5.4 2.7 - - - -
118Q LYS* 3.4 10.9 - - - +
119Q VAL* 1.3 82.4 - - - +
121Q GLU* 1.3 66.0 + - - +
139Q PRO* 3.6 1.2 - - - +
140Q GLN* 2.8 38.4 + - - +
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Residues in contact with GLU 121 (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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13660 C 6.2 0.4 - - - -
20540 A 4.9 4.9 + - - -
118Q LYS* 3.3 28.8 + - - -
120Q GLY* 1.3 79.0 - - - +
122Q GLN* 1.3 61.3 + - - +
123Q GLN* 3.1 17.0 + - + +
137Q ASN* 3.1 40.4 + - + +
138Q SER 3.1 10.8 - - - +
139Q PRO* 4.6 3.5 - - + +
140Q GLN* 3.6 7.6 + - - +
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Residues in contact with GLN 122 (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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14270 A 4.1 1.4 + - - +
14280 C 2.8 39.3 + - - +
14290 U 3.7 25.0 + - - +
22Q GLN* 3.0 23.5 + - - +
121Q GLU* 1.3 70.1 - - - +
123Q GLN* 1.3 68.5 + - - +
136Q TRP 4.7 0.2 - - - +
137Q ASN* 3.5 1.6 - - - -
138Q SER* 2.8 46.9 + - - +
140Q GLN* 4.0 20.8 + - + +
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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