Contacts of the strand formed by residues 13 - 21 (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 13 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8Q ALA* 3.4 29.0 - - + +
9Q ASP 2.8 23.9 + - - +
10Q PRO* 3.5 15.6 - - + +
11Q ASP 3.6 1.2 - - - -
12Q THR* 1.3 81.7 + - - +
14Q ALA* 1.3 69.5 + - - +
15Q LYS* 4.3 9.0 - - + -
102Q GLN* 3.7 12.1 - - - +
104Q PHE* 3.9 7.2 - - - -
109Q MET* 5.4 0.7 - - - -
112Q LYS* 5.0 2.4 + - - +
146Q ILE* 3.7 12.4 - - + +
147Q LEU 3.3 12.0 + - - -
148Q GLU* 4.3 8.5 + - - +
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Residues in contact with ALA 14 (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* 1.3 75.0 - - - +
15Q LYS* 1.3 63.4 + - - +
95Q ALA 4.4 2.5 - - - +
98Q ASN* 5.1 0.4 - - + -
99Q ALA* 3.9 37.0 - - + +
102Q GLN* 4.9 8.7 - - - +
104Q PHE* 5.1 2.0 - - + -
109Q MET* 4.3 4.4 - - - -
145Q LEU 3.9 0.2 - - - +
146Q ILE* 3.4 4.9 - - - +
147Q LEU* 2.7 52.2 + - + +
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Residues in contact with LYS 15 (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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5010 G 3.6 18.7 + - - +
5020 A 4.3 19.2 + - - +
4Q TYR* 3.3 52.9 - - + +
6Q VAL 5.6 0.8 + - - -
8Q ALA* 3.7 31.0 + - - +
13Q THR* 4.3 9.9 - - + -
14Q ALA* 1.3 78.1 - - - +
16Q ALA* 1.3 64.1 + - - +
95Q ALA* 4.2 3.2 - - - -
98Q ASN* 3.1 25.4 - - - +
102Q GLN* 5.5 1.2 - - - +
145Q LEU 3.3 4.9 - - - -
146Q ILE* 4.4 6.7 - - + -
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Residues in contact with ALA 16 (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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5000 G 3.5 8.5 - - - -
4Q TYR* 3.2 6.0 + - - -
15Q LYS* 1.3 80.9 - - - +
17Q MET* 1.3 67.4 + - - +
91Q LEU* 3.7 16.8 - - + +
94Q ASN* 3.6 15.5 - - - +
95Q ALA* 3.5 24.9 - - + -
144Q GLU* 3.6 0.3 - - - -
145Q LEU* 3.0 30.5 + - + +
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Residues in contact with MET 17 (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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4990 G 4.3 1.6 + - - -
5000 G 3.3 38.9 + - - +
5010 G 3.8 19.1 - - - +
2Q ILE* 3.9 26.7 - - - +
3Q SER* 5.2 2.5 - - - -
4Q TYR* 3.4 26.9 - - + +
16Q ALA* 1.3 83.4 - - - +
18Q LEU* 1.3 65.7 + - - +
19Q ARG* 2.9 45.3 - - - +
91Q LEU* 3.5 9.1 - - - +
94Q ASN* 5.2 1.7 + - - +
143Q VAL 3.1 13.0 - - - +
144Q GLU* 4.0 2.9 - - - -
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Residues in contact with LEU 18 (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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4990 G 4.7 1.3 - - - -
17Q MET* 1.3 80.3 - - - +
19Q ARG* 1.3 66.8 + - - +
21Q ARG* 3.8 39.0 - - + +
23Q MET* 4.5 4.5 - - + -
87Q ALA* 3.2 39.0 - - + +
88Q PHE* 4.4 3.1 - - + +
90Q ASP* 4.6 2.2 - - + -
91Q LEU* 3.7 26.5 - - + +
141Q VAL 4.3 0.7 - - - +
142Q ASP* 3.3 6.0 - - - +
143Q VAL* 3.0 51.4 + - + +
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Residues in contact with ARG 19 (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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4990 G 3.3 41.9 + - - +
5000 G 3.0 20.9 + - - +
1Q GLY* 3.6 6.6 - - - -
2Q ILE* 3.0 33.5 + - - +
3Q SER* 5.5 0.2 - - - +
17Q MET* 2.9 30.9 - - - +
18Q LEU* 1.3 80.4 - - - +
20Q GLU* 1.3 76.2 + - + +
21Q ARG* 3.1 12.3 + - - +
142Q ASP* 3.0 25.8 + - - -
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Residues in contact with GLU 20 (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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19Q ARG* 1.3 76.3 - - + +
21Q ARG* 1.3 65.1 + - - +
22Q GLN* 3.5 9.4 + - - +
119Q VAL* 4.9 14.8 - - + +
140Q GLN* 4.1 35.3 + - + +
141Q VAL 3.3 10.4 + - - +
142Q ASP* 2.7 19.7 + - - +
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Residues in contact with ARG 21 (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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4960 G 5.6 2.0 + - - -
4980 A 5.5 12.7 + - - -
18Q LEU* 3.8 44.2 - - + +
19Q ARG 3.1 10.6 + - - +
20Q GLU* 1.3 73.1 - - - +
22Q GLN* 1.3 61.3 + - - +
23Q MET* 3.2 32.2 + - + -
87Q ALA* 3.2 27.4 - - - +
90Q ASP* 3.3 27.3 + - - +
139Q PRO 3.3 0.2 - - - +
140Q GLN* 3.2 3.7 - - - -
141Q VAL* 2.7 41.7 + - - +
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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