Contacts of the helix formed by residues 22 - 32 (chain C) in PDB entry 1A81
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 ARG 22 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C THR* 1.3 76.9 + - - +
23C GLU* 1.3 69.6 + - - +
25C ALA* 2.8 23.6 + - - +
26C GLU* 3.2 17.3 + - - +
42C ARG* 3.7 20.2 - - - +
45C ARG* 5.2 1.0 - - - +
63C HIS* 3.4 38.2 - - + +
246C TYR* 3.9 1.4 + - - -
247C LYS* 4.0 4.7 - - - +
179D ASP* 3.2 41.0 + - - +
180D LEU 2.3 31.3 + - - +
181D PTR 3.0 62.8 + - - +
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Residues in contact with GLU 23 (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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185A GLY* 4.2 6.6 - - - +
186A SER* 4.0 31.2 - - - +
187A LYS* 3.9 18.6 - - + +
21C THR* 3.2 4.0 + - + +
22C ARG* 1.3 81.7 - - + +
24C GLU* 1.3 62.4 + - - +
25C ALA 3.0 1.0 + - - -
26C GLU* 3.2 13.3 + - - +
27C ASP* 3.1 26.7 + - - +
246C TYR* 2.9 23.7 + - - -
247C LYS* 2.7 32.2 + - - +
179D ASP* 3.0 11.6 - - - +
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Residues in contact with GLU 24 (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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20C ILE* 3.7 16.6 - - + +
21C THR* 2.6 46.0 + - + +
23C GLU* 1.3 73.9 - - - +
25C ALA* 1.3 51.3 + - - +
27C ASP* 3.2 21.9 - - - +
28C TYR* 2.7 40.3 + - + -
116C LYS* 2.8 37.6 + - - -
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Residues in contact with ALA 25 (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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17C PHE* 6.0 0.2 - - - -
20C ILE* 3.7 10.7 - - + +
21C THR 3.2 7.1 + - - +
22C ARG 2.8 12.2 + - - +
24C GLU* 1.3 74.6 - - - +
26C GLU* 1.3 67.7 + - - +
27C ASP 2.8 1.6 - - - -
28C TYR* 2.8 15.3 + - - +
29C LEU* 2.8 26.4 + - - +
40C LEU* 4.1 22.3 - - + +
42C ARG* 4.6 5.4 - - - +
54C SER* 4.4 13.7 - - - +
63C HIS* 4.7 1.3 - - + -
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Residues in contact with GLU 26 (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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183A LEU 4.1 2.1 - - - +
184A ILE* 3.4 18.3 - - + +
185A GLY* 3.0 34.4 + - - +
22C ARG* 3.7 22.7 + - - +
23C GLU* 3.2 10.3 + - - +
25C ALA* 1.3 74.3 - - - +
27C ASP* 1.3 67.4 + - - +
29C LEU* 3.1 21.8 + - - +
30C VAL* 3.1 18.5 + - - +
61C ALA* 4.2 12.4 - - + +
63C HIS* 3.4 32.5 + - + +
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Residues in contact with ASP 27 (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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185A GLY* 3.5 20.8 - - - -
186A SER* 4.3 6.0 + - - -
260A GLN* 5.7 7.5 - - - +
23C GLU* 3.1 16.9 + - - +
24C GLU* 3.2 19.0 - - - +
25C ALA 2.8 1.0 - - - -
26C GLU* 1.3 77.1 - - - +
28C TYR* 1.3 54.1 + - + +
30C VAL* 2.8 14.9 + - - +
31C GLN* 2.5 38.0 + - + -
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Residues in contact with TYR 28 (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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17C PHE* 4.4 15.0 - + - +
20C ILE* 4.5 19.6 - - + +
24C GLU* 2.7 44.6 + - + -
25C ALA* 2.8 14.4 + - - +
27C ASP* 1.3 76.3 - - + +
29C LEU* 1.3 51.6 + - - +
31C GLN* 3.3 17.7 - - + -
32C GLY 2.5 32.4 + - - -
40C LEU* 3.9 16.4 - - + -
107C PHE* 2.9 31.9 - + + -
110C PRO* 4.0 24.0 - - + -
113C VAL* 4.4 15.9 - - + +
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Residues in contact with LEU 29 (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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25C ALA 2.8 22.5 + - - +
26C GLU* 3.4 15.0 - - - +
27C ASP 2.9 0.2 + - - -
28C TYR* 1.3 72.3 - - - +
30C VAL* 1.3 52.5 + - - +
32C GLY* 2.7 3.1 + - - -
33C GLY 2.6 32.1 + - - -
34C MET* 2.8 21.5 + - + -
38C LEU* 3.5 37.8 - - + +
39C TYR* 4.5 2.9 - - - -
40C LEU* 4.1 20.9 - - + -
54C SER* 4.2 30.7 - - - +
55C VAL 4.5 2.0 - - - +
56C ALA* 4.4 12.1 - - + +
61C ALA* 4.5 13.0 - - + -
63C HIS* 5.5 0.4 - - + -
107C PHE* 4.6 2.2 - - + -
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Residues in contact with VAL 30 (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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181A ILE* 5.2 5.8 - - + -
184A ILE* 3.4 32.8 - - + -
260A GLN* 5.2 15.3 - - + -
261A LYS 5.4 1.8 - - - +
262A ILE* 3.5 35.9 - - + +
26C GLU 3.3 12.3 - - - +
27C ASP* 2.8 22.1 + - - +
29C LEU* 1.3 67.0 - - - +
31C GLN* 1.3 74.4 + - + +
32C GLY 2.6 15.4 + - - -
33C GLY 2.9 11.2 + - - +
34C MET* 3.6 22.2 - - + +
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Residues in contact with GLN 31 (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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262A ILE 5.1 7.3 - - - +
27C ASP* 2.5 20.8 + - + +
28C TYR* 3.1 33.5 - - + +
30C VAL* 1.3 77.4 - - + +
32C GLY* 1.3 55.2 + - - +
107C PHE* 4.0 16.1 - - + -
110C PRO* 5.2 7.4 - - - +
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Residues in contact with GLY 32 (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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262A ILE 5.9 0.4 - - - -
28C TYR 2.5 10.3 + - - -
29C LEU 2.7 4.0 + - - -
30C VAL 2.6 5.4 + - - -
31C GLN* 1.3 75.8 - - - +
33C GLY* 1.3 55.4 + - - -
34C MET 3.9 0.2 - - - -
35C SER* 5.6 0.3 - - - -
38C LEU* 4.5 7.5 - - - +
107C PHE* 3.0 27.1 - - - -
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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