Contacts of the helix formed by residues 10 - 20 (chain C) in PDB entry 1XPU
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 PRO 10 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C ASN 3.8 5.8 - - - +
9C THR* 1.3 88.8 - - + +
11C VAL* 1.3 61.0 + - - +
12C SER* 3.3 13.9 - - - +
13C GLU* 3.2 31.3 + - + +
14C LEU* 2.9 23.9 + - - +
31C LYS* 5.0 2.0 - - - +
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Residues in contact with VAL 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LYS* 4.8 7.4 - - + -
134B GLU* 3.8 49.4 - - + +
9C THR 3.6 0.9 + - - -
10C PRO* 1.3 72.0 - - - +
12C SER* 1.3 62.9 + - - +
14C LEU* 3.1 8.5 + - + +
15C ILE* 3.1 45.1 + - + +
31C LYS* 3.8 31.6 - - + +
34C ILE* 4.6 6.7 - - + -
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Residues in contact with SER 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LYS* 3.8 28.6 + - - +
10C PRO* 4.1 8.3 - - - +
11C VAL* 1.3 79.7 - - - +
13C GLU* 1.3 75.5 + - - +
15C ILE* 3.7 5.0 + - - +
16C THR* 3.4 24.3 + - - +
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Residues in contact with GLU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C THR* 4.7 8.6 - - - +
10C PRO* 3.2 35.8 + - + +
11C VAL 3.2 0.4 - - - -
12C SER* 1.3 87.9 + - - +
14C LEU* 1.3 65.7 + - - +
15C ILE 3.2 0.4 - - - -
16C THR* 2.6 24.9 + - - +
17C LEU* 3.2 11.2 + - - +
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Residues in contact with LEU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 3.3 39.5 - - + +
9C THR* 3.5 27.3 + - - +
10C PRO 2.9 12.8 + - - +
11C VAL* 3.1 7.8 + - + +
13C GLU* 1.3 76.6 - - - +
15C ILE* 1.3 61.8 + - + +
17C LEU* 3.7 8.3 - - + +
18C GLY 3.5 14.0 + - - -
31C LYS* 3.8 19.3 - - + +
34C ILE* 3.8 20.2 - - + -
35C ILE* 3.5 23.1 - - + -
38C ILE* 3.9 16.8 - - + +
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Residues in contact with ILE 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LYS* 4.3 15.0 - - + +
11C VAL* 3.1 30.4 + - + +
12C SER* 3.9 7.6 - - - +
13C GLU 3.2 0.4 - - - -
14C LEU* 1.3 75.6 - - - +
16C THR* 1.3 61.3 + - + +
18C GLY* 3.1 4.3 + - - -
19C GLU* 2.9 45.9 + - + +
26C LEU* 4.1 20.9 - - + +
27C ALA* 4.0 33.0 - - + +
34C ILE* 3.9 26.0 - - + -
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Residues in contact with THR 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C SER 3.4 14.8 - - - +
13C GLU* 2.6 25.4 + - - +
15C ILE* 1.3 74.8 - - + +
17C LEU* 1.3 65.0 + - - +
19C GLU* 3.2 17.8 + - - +
20C ASN* 3.1 37.7 + - - +
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Residues in contact with LEU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 6.6 0.2 - - + -
6C LEU* 4.7 14.4 - - + -
9C THR* 6.3 3.4 - - + -
13C GLU 3.2 8.2 + - - +
14C LEU* 3.7 13.0 - - + +
16C THR* 1.3 82.5 + - - +
18C GLY* 1.3 60.7 + - - +
20C ASN* 3.6 12.7 + - - +
21C MET* 3.3 30.7 + - + +
38C ILE* 3.8 31.2 - - + -
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Residues in contact with GLY 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU 3.5 4.6 + - - -
15C ILE 3.1 7.6 + - - -
17C LEU* 1.3 76.2 - - - +
19C GLU* 1.3 58.2 + - - +
20C ASN 3.1 2.0 - - - -
21C MET* 2.9 21.6 + - - +
23C LEU* 3.2 32.9 + - - +
26C LEU* 4.5 3.1 - - - -
38C ILE* 4.0 22.7 - - - -
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Residues in contact with GLU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ILE* 2.9 34.0 + - + +
16C THR* 3.2 23.1 + - - +
18C GLY* 1.3 75.3 - - - +
20C ASN* 1.3 61.9 + - - +
21C MET 3.1 3.4 + - - -
22C GLY* 3.5 11.0 + - - -
23C LEU 3.6 17.5 - - - +
25C ASN 5.9 2.1 + - - +
26C LEU* 4.6 7.5 + - + +
27C ALA* 5.6 4.7 + - - +
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Residues in contact with ASN 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C THR* 3.1 25.0 + - - +
17C LEU* 3.9 8.0 - - - +
18C GLY 3.1 0.4 - - - -
19C GLU* 1.3 80.7 - - - +
21C MET* 1.3 61.8 + - - +
22C GLY 3.5 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