Contacts of the strand formed by residues 88 - 100 (chain Q) in PDB entry 4R2G
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 ALA 88 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38Q ARG* 4.1 5.2 - - - -
39Q GLN 3.4 25.6 - - - +
40Q SER* 3.4 16.4 - - - +
41Q PRO* 4.7 2.5 - - - -
86Q ASP 3.3 4.0 + - - +
87Q THR* 1.3 76.8 - - - +
89Q ILE* 1.3 64.9 + - - +
90Q TYR* 3.3 22.1 - - + -
108Q ALA* 5.3 0.2 - - - -
109Q VAL 2.9 31.2 + - - -
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Residues in contact with ILE 89 (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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41P GLY* 4.6 26.0 - - - +
39Q GLN* 3.5 32.4 + - + +
88Q ALA* 1.3 78.3 - - - +
90Q TYR* 1.3 57.8 + - - +
91Q PHE* 3.2 44.8 - - + -
105Q LYS 5.1 0.9 - - - +
106Q GLY* 4.2 2.9 - - - -
107Q THR 3.4 21.8 - - - +
108Q ALA* 4.1 19.1 - - + -
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Residues in contact with TYR 90 (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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6Q GLU* 4.0 3.1 - - - +
18Q LEU* 4.1 19.7 - - + +
20Q VAL* 4.3 20.4 - - + -
36Q TRP* 4.3 5.8 - + + -
37Q ILE 3.9 2.9 - - - -
38Q ARG* 2.8 43.5 + - + +
48Q ILE* 4.4 6.3 - - + -
80Q LEU* 3.9 26.9 - - + -
82Q LEU* 3.7 15.4 - - + +
86Q ASP* 2.7 28.8 + - - +
88Q ALA* 3.3 23.3 - - + -
89Q ILE* 1.3 72.9 - - - +
91Q PHE* 1.3 59.6 + - - +
106Q GLY* 3.4 1.9 - - - -
107Q THR* 2.8 42.1 + - + +
109Q VAL* 4.0 13.2 - - + -
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Residues in contact with PHE 91 (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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38P HIS* 4.8 2.5 - - - -
41P GLY 5.3 0.7 - - - -
42P GLN 3.7 17.0 - - - -
43P ALA* 3.5 25.1 - - + -
44P PRO* 4.1 9.4 - - + -
6Q GLU* 3.2 4.9 - - - +
36Q TRP* 3.3 8.7 - - - -
37Q ILE* 2.8 45.2 + - + +
38Q ARG 4.7 2.5 - - - -
39Q GLN* 4.3 15.7 - - + -
45Q LEU* 5.0 2.0 - - + -
89Q ILE* 3.2 46.0 - - + -
90Q TYR* 1.3 74.4 - - - +
92Q CYS* 1.3 61.4 + - - +
103Q TRP* 3.9 25.6 - + + -
104Q GLY 3.7 16.6 - - - -
105Q LYS 3.5 15.9 - - - -
106Q GLY* 3.8 7.9 - - - -
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Residues in contact with CYS 92 (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 LEU* 3.5 10.1 - - - -
6Q GLU* 2.5 20.8 + - - +
22Q CYS* 2.0 56.3 - - + -
35Q THR 3.2 6.7 - - - +
36Q TRP* 3.8 21.0 - - + -
78Q LEU* 4.5 9.2 - - + -
91Q PHE* 1.3 77.7 - - - +
93Q ALA* 1.3 65.1 + - - +
104Q GLY 2.9 24.9 + - - -
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Residues in contact with ALA 93 (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 LEU* 3.5 5.0 - - - +
34Q TRP* 3.6 9.1 - - - -
35Q THR* 2.9 35.2 + - + +
37Q ILE* 4.9 2.2 - - + -
92Q CYS* 1.3 78.3 - - - +
94Q THR* 1.3 67.3 + - - +
95Q ALA 3.5 0.2 + - - -
100Q MET* 4.2 12.3 - - - +
102Q VAL 3.1 17.3 - - - +
103Q TRP* 3.9 24.0 - - + -
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Residues in contact with THR 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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2Q VAL* 4.5 1.7 - - - +
4Q LEU* 4.1 2.7 - - - +
32Q TYR* 4.1 16.1 - - + -
33Q TYR 3.8 7.2 - - - +
34Q TRP* 3.7 20.6 - - - -
93Q ALA* 1.3 75.2 - - - +
95Q ALA* 1.3 64.2 + - - +
96Q ARG* 3.2 41.1 - - + +
100Q MET* 3.3 27.0 + - - -
101Q ASP* 3.3 13.8 + - - +
102Q VAL* 2.9 24.5 + - - +
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Residues in contact with ALA 95 (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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33Q TYR* 3.1 47.9 + - + +
34Q TRP 4.7 0.7 - - - +
35Q THR* 3.8 24.9 - - + -
47Q TRP* 5.8 1.1 - - + -
50Q TYR* 5.1 5.6 - - + -
93Q ALA 3.5 0.4 + - - -
94Q THR* 1.3 74.5 - - - +
96Q ARG* 1.3 68.4 + - - +
100Q TYR* 3.5 25.1 - - + +
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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
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2Q VAL* 5.6 0.2 - - - +
32Q TYR* 4.6 14.6 - - - -
33Q TYR* 5.5 0.4 - - - -
94Q THR* 3.2 22.3 - - + +
95Q ALA* 1.3 77.2 - - - +
97Q ARG* 1.3 60.9 - - - +
98Q GLY 3.5 2.0 + - - -
100Q TYR* 2.9 76.5 + - + +
101Q ASP* 2.6 40.5 + - - +
102Q VAL* 4.1 6.1 - - - +
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Residues in contact with ARG 97 (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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9G MAN 4.3 9.5 + - - -
33Q TYR* 3.7 34.0 + - + -
54Q ARG* 5.2 11.0 - - - +
95Q ALA 4.2 0.6 + - - -
96Q ARG* 1.3 71.2 - - - +
98Q GLY* 1.3 59.2 + - - +
99Q GLN 4.2 0.2 + - - -
100Q TYR* 3.3 98.2 + - + +
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Residues in contact with GLY 98 (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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9G MAN 4.5 5.2 - - - -
96Q ARG 3.5 4.2 + - - -
97Q ARG* 1.3 75.2 - - - +
99Q GLN* 1.3 60.3 + - - +
100Q TYR* 2.9 69.0 + - - +
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Residues in contact with GLN 99 (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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7G MAN 5.9 2.3 - - - -
9G MAN 3.0 48.0 + - - +
98Q GLY* 1.3 75.0 - - - +
100Q TYR* 1.3 154.8 + - + +
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Residues in contact with ARG 100 (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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4G MAN 2.9 38.3 + - - -
5G MAN 2.9 51.9 + - - -
30P SER* 4.5 6.6 - - - -
31P ARG 2.9 22.4 + - - +
32P ALA* 4.2 3.8 - - + -
50P ASN* 4.6 3.1 - - - -
66P ASP* 2.8 29.6 + - - +
99Q GLN* 1.3 69.3 - - - +
100Q PHE* 1.3 159.8 + - - +
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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