Contacts of the strand formed by residues 138 - 148 (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 SER 138 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20530 G 2.4 27.3 + - - -
22Q GLN* 4.2 16.2 + - - -
121Q GLU* 3.1 5.5 - - - -
122Q GLN* 2.8 56.8 + - - +
136Q TRP 5.1 0.9 + - - -
137Q ASN* 1.3 76.0 - - - +
139Q PRO* 1.3 73.6 - - - +
140Q GLN* 4.0 0.3 - - - +
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Residues in contact with PRO 139 (chain Q).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13700 G 3.5 28.9 - - + +
20530 G 4.4 8.5 - - - +
20540 A 5.6 1.8 - - - +
21Q ARG 3.3 1.4 - - - +
22Q GLN* 3.3 23.8 - - - +
23Q MET 3.6 20.2 + - - +
25Q PHE* 4.4 15.7 - - + +
118Q LYS* 4.0 25.4 - - - +
120Q GLY 3.6 6.5 - - - +
121Q GLU* 4.5 2.0 - - + +
137Q ASN 4.3 3.8 - - - +
138Q SER* 1.3 87.8 - - - +
140Q GLN* 1.3 61.6 + - - +
141Q VAL* 4.7 0.9 - - + -
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Residues in contact with GLN 140 (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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20Q GLU* 4.1 40.0 + - + +
21Q ARG 3.2 4.0 - - - -
22Q GLN* 4.5 16.3 - - + +
118Q LYS* 3.6 5.0 - - - +
119Q VAL* 2.8 29.7 + - - +
120Q GLY* 2.8 22.2 + - - +
121Q GLU 3.6 17.4 + - - +
122Q GLN* 4.0 25.2 + - - +
138Q SER 4.0 5.6 - - - +
139Q PRO* 1.3 79.0 - - - +
141Q VAL* 1.3 60.9 + - - +
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Residues in contact with VAL 141 (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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18Q LEU* 4.1 1.9 - - - +
19Q ARG 3.8 1.2 - - - -
20Q GLU 3.3 2.9 + - - -
21Q ARG* 2.7 43.6 + - - +
23Q MET* 3.9 37.2 - - + +
25Q PHE* 3.7 38.4 - - + -
28Q SER* 4.2 1.8 - - - +
116Q ALA* 3.9 19.3 - - + -
117Q HIS 3.5 6.5 - - - +
118Q LYS* 4.8 0.2 - - - -
139Q PRO* 4.7 0.2 - - + -
140Q GLN* 1.3 80.2 - - - +
142Q ASP* 1.3 80.5 + - - +
143Q VAL* 4.8 0.7 - - + -
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Residues in contact with ASP 142 (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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1Q GLY* 3.3 5.4 - - - -
2Q ILE* 3.0 31.5 + - + -
18Q LEU 3.3 9.4 - - - +
19Q ARG* 3.0 32.3 + - - -
20Q GLU* 2.7 35.3 + - - +
117Q HIS 2.9 29.2 + - - +
119Q VAL* 3.3 22.7 - - + +
141Q VAL* 1.3 79.5 - - - +
143Q VAL* 1.3 61.4 + - - +
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Residues in contact with VAL 143 (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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2Q ILE* 4.2 4.3 - - - -
17Q MET* 3.1 9.5 - - - +
18Q LEU* 3.0 71.0 + - + -
23Q MET* 4.9 6.7 - - + -
88Q PHE* 4.2 20.0 - - + -
91Q LEU* 3.7 18.6 - - + +
114Q VAL* 4.5 0.7 - - + -
115Q ALA 3.2 23.6 - - - +
116Q ALA* 4.2 5.6 - - + +
141Q VAL* 4.8 1.8 - - + +
142Q ASP* 1.3 78.9 - - - +
144Q GLU* 1.3 67.3 + - - +
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Residues in contact with GLU 144 (chain Q).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2Q ILE* 4.0 16.2 - - + -
3Q SER 4.5 0.7 - - - -
4Q TYR* 3.4 25.9 - - + +
5Q SER* 2.5 43.2 + - - -
6Q VAL 4.4 0.3 + - - -
16Q ALA 3.6 4.3 - - - -
17Q MET* 4.0 2.2 - - + -
113Q HIS* 3.1 28.2 + - + +
114Q VAL* 3.2 5.4 - - - -
115Q ALA* 3.0 33.4 + - - +
117Q HIS* 3.1 20.6 - - + -
143Q VAL* 1.3 78.9 - - - +
145Q LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 145 (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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4Q TYR* 4.1 0.5 - - - -
14Q ALA 3.9 0.2 - - - +
15Q LYS* 3.3 6.1 - - - +
16Q ALA* 3.0 36.3 + - + +
35Q ILE* 5.9 1.3 - - + -
91Q LEU* 3.9 28.9 - - + -
92Q LEU* 3.5 35.0 - - + -
95Q ALA* 4.1 17.0 - - + -
111Q ILE* 3.2 30.7 - - + -
113Q HIS 3.2 16.4 - - - +
114Q VAL* 3.9 9.2 - - + -
144Q GLU* 1.3 77.7 - - - +
146Q ILE* 1.3 72.9 + - - +
147Q LEU* 4.1 5.8 - - + -
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Residues in contact with ILE 146 (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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4Q TYR* 4.2 22.2 - - + -
6Q VAL* 3.9 33.0 - - + +
7Q GLU 4.7 0.2 - - - +
8Q ALA* 4.1 18.4 - - + -
13Q THR* 3.7 22.4 - - + +
14Q ALA 3.4 6.1 - - - +
15Q LYS* 4.4 5.4 - - + -
111Q ILE* 3.7 2.3 - - - -
112Q LYS* 2.8 41.4 + - + +
113Q HIS* 2.8 37.7 + - + +
145Q LEU* 1.3 78.8 - - - +
147Q LEU* 1.3 62.7 + - - +
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Residues in contact with LEU 147 (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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13Q THR* 3.3 10.0 + - - -
14Q ALA* 2.7 41.3 + - + +
40Q ALA* 4.1 15.5 - - + -
92Q LEU* 4.9 0.7 - - + -
95Q ALA* 3.5 44.6 - - + +
96Q VAL* 3.8 13.7 - - + +
99Q ALA* 4.4 5.6 - - + -
106Q GLY 4.6 0.7 - - - +
109Q MET* 3.9 22.0 - - + +
110Q THR 3.2 12.6 - - - +
111Q ILE* 4.0 22.2 - - + -
145Q LEU* 4.6 10.5 - - + -
146Q ILE* 1.3 74.1 - - - +
148Q GLU* 1.3 59.7 + - - +
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Residues in contact with GLU 148 (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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12Q THR* 3.4 21.1 + - - +
13Q THR* 4.3 6.2 + - - +
109Q MET* 3.5 5.9 - - - +
110Q THR* 2.8 42.1 + - - +
112Q LYS* 3.9 45.0 + - + +
147Q LEU* 1.3 78.0 - - - +
149Q GLU* 1.3 77.1 - - - +
150Q PRO 3.5 0.2 - - - -
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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