Contacts of the helix formed by residues 8 - 16 (chain J) in PDB entry 1RQF
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 8 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6J GLU 3.6 2.8 + - - -
7J VAL* 1.3 76.0 - - - +
9J TRP* 1.3 60.4 + - - +
10J ILE* 4.0 8.3 + - - +
11J SER* 3.1 27.1 + - - -
12J TRP* 2.8 27.4 + - - +
24J GLU* 4.7 1.4 + - - -
55J ASP* 3.4 17.3 - - - -
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Residues in contact with TRP 9 (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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7J VAL 3.7 0.6 + - - -
8J SER* 1.3 73.0 - - - +
10J ILE* 1.3 64.5 + - + +
12J TRP* 3.1 34.0 + + - +
13J PHE* 2.7 65.8 + + + -
52J MET* 3.3 45.5 - - + +
53J ILE* 3.7 18.2 - - + +
55J ASP* 3.1 17.8 + - - +
73J GLU* 5.0 2.4 + - - +
76J ALA* 3.9 26.2 - - + -
77J GLU* 4.3 5.8 - - + -
80J TYR* 3.6 41.7 - + + -
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Residues in contact with ILE 10 (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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8J SER* 3.2 7.3 + - - +
9J TRP* 1.3 92.1 - - + +
11J SER* 1.3 62.9 + - - +
13J PHE* 3.2 1.0 + - - -
14J CYS* 2.9 25.7 + - - -
24J GLU* 3.9 24.7 - - + +
25J VAL 3.7 14.1 - - - +
27J GLU* 5.1 7.9 - - + -
30J ILE* 3.6 30.1 - - + -
53J ILE* 3.8 19.1 - - + +
54J LEU* 5.3 2.5 - - + -
80J TYR* 3.7 30.1 - - + +
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Residues in contact with SER 11 (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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7J VAL* 4.6 11.4 - - - +
8J SER* 3.1 27.6 + - - -
10J ILE* 1.3 79.1 - - - +
12J TRP* 1.3 62.9 + - - +
14J CYS* 4.1 1.4 - - - +
15J GLY* 3.2 18.4 + - - -
24J GLU* 3.5 28.5 + - - +
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Residues in contact with TRP 12 (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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7J VAL* 4.4 20.8 - - + +
8J SER 2.8 13.0 + - - +
9J TRP* 3.4 52.3 - + - +
11J SER* 1.3 77.4 - - - +
13J PHE* 1.3 80.9 + + + +
15J GLY* 3.2 9.6 + - - -
16J LEU* 3.3 48.5 + - + +
73J GLU* 6.0 2.0 - - - -
77J GLU* 6.1 1.3 - - - -
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Residues in contact with PHE 13 (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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9J TRP* 2.7 48.0 + + + +
10J ILE* 3.6 3.4 - - - +
12J TRP* 1.3 83.6 - + + +
14J CYS* 1.3 64.2 + - - +
15J GLY 2.8 10.8 + - - -
16J LEU* 2.9 19.9 + - + +
19J ASN* 3.0 41.3 + - - -
22J PHE* 4.0 28.0 - + - -
77J GLU* 3.5 39.5 - - + -
80J TYR* 3.6 36.3 - + - -
81J GLY* 6.0 0.4 - - - -
158J TYR* 6.4 0.7 - + - -
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Residues in contact with CYS 14 (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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10J ILE 2.9 16.9 + - - +
11J SER 4.3 1.6 - - - +
13J PHE* 1.3 81.7 - - - +
15J GLY* 1.3 59.1 + - - +
16J LEU 3.8 0.3 + - - +
19J ASN* 3.4 24.5 - - - +
20J GLU* 4.7 2.1 + - - -
22J PHE* 4.2 14.4 - - + +
23J CYS 3.6 15.0 - - - -
24J GLU* 3.7 23.3 - - + +
80J TYR* 3.5 35.2 - - - -
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Residues in contact with GLY 15 (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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11J SER 3.2 10.6 + - - -
12J TRP 3.2 8.8 + - - -
13J PHE 2.8 1.8 + - - -
14J CYS* 1.3 77.7 - - - +
16J LEU* 1.3 65.3 + - - +
17J ARG 3.8 0.5 + - - -
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Residues in contact with LEU 16 (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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12J TRP* 3.3 57.4 + - + +
13J PHE* 2.9 21.1 + - + +
14J CYS 4.2 0.5 - - - +
15J GLY* 1.3 81.9 - - - +
17J ARG* 1.3 67.5 + - - +
18J GLY 3.3 0.5 + - - -
19J ASN* 3.1 36.0 + - - +
20J GLU* 4.4 3.6 + - - +
77J GLU* 6.0 1.3 - - - +
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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