Contacts of the helix formed by residues 17 - 28 (chain J) in PDB entry 5T0G
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 PHE 17 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8J THR* 4.5 3.4 - - + +
9J VAL* 4.2 27.3 + - + +
11J SER* 3.3 34.5 - - - -
12J PRO* 5.5 1.1 - - + -
13J ASP* 4.9 5.2 - - - -
16J LEU* 1.3 84.2 - - - +
18J GLN* 1.3 74.8 + - + +
19J VAL 3.1 1.2 + - - -
20J GLU* 3.5 1.6 + - - +
21J TYR* 2.9 35.3 + - - +
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Residues in contact with GLN 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I ILE* 3.4 29.9 - - + +
12I PHE* 3.1 37.0 + - + +
14I PRO* 5.6 7.9 - - - +
7J ILE* 4.5 9.9 - - + +
8J THR* 3.7 21.7 - - - +
17J PHE* 1.3 88.9 - - + +
19J VAL* 1.3 57.3 + - - +
21J TYR* 3.2 23.0 - - - +
22J ALA* 2.9 30.1 + - - +
126J PRO* 4.4 14.9 - - + +
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Residues in contact with VAL 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J THR* 3.8 18.4 - - + +
16J LEU* 3.7 25.8 - - + -
17J PHE 3.1 0.6 - - - -
18J GLN* 1.3 73.8 - - - +
20J GLU* 1.3 78.3 + - - +
22J ALA* 2.9 25.4 + - - +
23J GLN* 3.8 2.8 + - - -
119J THR* 4.7 20.0 - - + -
126J PRO* 4.7 5.4 - - + -
149J PRO* 3.9 13.2 - - + +
150J SER* 4.2 34.5 - - - +
81K LEU* 6.0 1.3 - - + -
135K ARG* 5.5 0.9 - - - +
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Residues in contact with GLU 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J HIS* 4.3 22.3 - - + +
16J LEU* 3.1 54.9 + - - +
17J PHE 3.5 0.6 + - - +
19J VAL* 1.3 82.5 - - + +
21J TYR* 1.3 61.6 + - - +
23J GLN* 3.3 35.0 + - - +
24J GLU* 4.2 6.8 - - - +
81K LEU* 5.2 9.7 - - - +
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Residues in contact with TYR 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I PHE* 3.2 24.4 - + + +
13I SER 2.1 28.5 + - - -
14I PRO* 3.0 38.4 - - + -
15I GLU 4.3 0.2 - - - -
16I GLY* 3.2 25.2 + - - -
17J PHE 2.9 19.3 + - - +
18J GLN* 3.2 37.9 - - - +
20J GLU* 1.3 74.4 - - - +
22J ALA* 1.3 69.6 + - - +
24J GLU* 3.1 30.1 + - + +
25J ALA* 4.1 2.8 + - + +
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Residues in contact with ALA 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I PHE* 5.3 3.8 - - + -
18J GLN 2.9 22.1 + - - +
19J VAL* 2.9 11.1 + - - +
21J TYR* 1.3 82.4 - - + +
23J GLN* 1.3 59.9 + - - +
25J ALA* 3.1 15.0 + - - +
26J VAL* 3.6 1.9 + - - +
126J PRO* 5.5 1.3 - - + -
127J PHE 3.4 25.4 - - - +
128J GLY* 3.3 24.8 - - - +
149J PRO* 4.3 9.2 - - + -
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Residues in contact with GLN 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J VAL* 4.5 2.0 - - - +
20J GLU* 3.5 27.7 - - - +
21J TYR 3.1 1.2 - - - -
22J ALA* 1.3 76.6 - - - +
24J GLU* 1.3 63.7 + - - +
26J VAL* 3.2 13.5 + - + +
27J LYS* 3.0 24.9 + - - +
148J ASP* 3.9 24.7 + - - -
149J PRO* 3.7 19.7 - - + +
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Residues in contact with GLU 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I PRO 5.9 0.4 - - - +
15I GLU 6.1 0.2 - - - -
16I GLY* 5.4 0.2 - - - -
20J GLU 4.2 8.0 - - - +
21J TYR* 3.1 32.0 + - + +
23J GLN* 1.3 81.4 - - - +
25J ALA* 1.3 59.8 + - - +
27J LYS* 3.1 12.1 + - - +
28J LYS* 2.8 48.1 + - - +
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Residues in contact with ALA 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I PHE* 6.5 0.9 - - + -
16I GLY* 4.8 12.7 - - - +
21J TYR* 4.1 2.4 + - + -
22J ALA* 3.1 8.9 + - - +
24J GLU* 1.3 79.2 - - - +
26J VAL* 1.3 55.3 + - - +
28J LYS* 3.2 14.7 + - - +
29J GLY* 3.0 24.4 + - - -
75J GLY* 4.5 4.0 - - - -
76J LEU* 5.0 13.6 + - + -
128J GLY* 3.2 26.2 - - - +
129J ILE* 5.8 0.2 - - + -
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Residues in contact with VAL 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J ALA 3.8 7.4 - - - +
23J GLN* 3.2 13.3 + - + +
25J ALA* 1.3 73.0 - - - +
27J LYS* 1.3 65.6 + - - +
29J GLY* 3.3 9.9 + - - +
30J SER 4.8 0.7 - - - +
74J ALA* 4.8 15.0 - - + -
75J GLY* 4.8 7.0 + - - +
128J GLY 3.1 20.4 - - - +
129J ILE* 3.5 16.6 - - - -
130J SER* 3.7 27.4 - - - +
149J PRO* 5.0 2.2 - - + -
161J ILE* 5.4 7.9 - - + -
162J GLY* 3.8 21.3 - - - +
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Residues in contact with LYS 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J GLN 3.0 13.5 + - - +
24J GLU* 3.1 17.9 + - - +
26J VAL* 1.3 78.1 - - - +
28J LYS* 1.3 60.4 + - + +
162J GLY 4.3 9.9 - - - +
163J ARG* 3.4 27.4 + - - +
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Residues in contact with LYS 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I GLU 3.9 9.2 + - - +
16I GLY* 3.6 32.2 - - - -
24J GLU* 2.8 53.1 + - - +
25J ALA* 3.2 10.5 + - - +
26J VAL 3.2 0.2 - - - -
27J LYS* 1.3 76.9 - - + +
29J GLY* 1.3 62.4 + - - +
163J ARG* 5.7 0.7 - - - -
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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