Contacts of the helix formed by residues 15 - 23 (chain A) in PDB entry 3GUU
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 ASN 15 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A PRO* 1.3 75.0 - - - +
16A PRO* 1.3 64.2 - - - +
17A TYR* 2.9 39.0 + - - +
18A ASP* 2.8 35.2 + - - +
19A ASP* 3.5 4.2 + - - +
100A ASP* 2.9 27.3 + - - +
105A TYR* 3.9 18.7 + - - +
114A PRO* 5.4 1.2 - - - +
270A ARG* 3.2 34.5 - - - +
224B PHE* 4.9 4.4 - - - -
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Residues in contact with PRO 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO 3.4 1.1 - - - +
15A ASN* 1.3 90.5 - - - +
17A TYR* 1.3 61.3 + - - +
19A ASP* 3.1 22.7 + - + +
22A TYR* 3.6 42.1 - - + +
99A LEU* 3.7 25.7 - - + +
100A ASP* 3.7 10.8 - - + -
102A ALA* 5.2 0.4 - - + -
105A TYR* 3.5 46.4 - - + -
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Residues in contact with TYR 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASN* 2.9 23.6 + - - +
16A PRO* 1.3 79.9 - - - +
18A ASP* 1.3 58.9 + - - +
19A ASP 3.3 1.3 + - - +
98A ALA* 3.6 11.3 - - - +
99A LEU* 2.9 37.1 + - + +
100A ASP* 3.5 26.5 - - - -
268A ARG 3.8 11.9 + - - -
270A ARG* 3.4 48.1 + - + +
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Residues in contact with ASP 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO* 4.2 6.4 - - + +
15A ASN* 2.8 20.0 + - - +
17A TYR* 1.3 73.9 - - - +
19A ASP* 1.3 57.6 + - - +
20A PRO* 3.9 1.5 - - - +
270A ARG* 2.9 33.9 + - - -
332B ILE* 3.4 38.6 - - + +
333B PRO* 3.4 23.8 - - - +
339B TYR* 4.7 4.8 - - - +
340B GLN* 2.9 31.5 + - - +
362B PRO 4.7 0.7 - - - +
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Residues in contact with ASP 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.8 0.7 - - - +
14A PRO* 3.8 24.5 - - + +
15A ASN 3.7 9.0 - - - +
16A PRO* 3.1 21.5 + - + +
17A TYR 3.3 2.0 + - - -
18A ASP* 1.3 77.6 - - - +
20A PRO* 1.4 69.1 - - - +
21A PHE* 3.2 18.2 + - - +
22A TYR* 2.9 27.7 + - + +
23A THR* 4.4 2.7 - - - +
40A ARG* 3.0 35.8 + - - -
333B PRO* 4.4 3.5 - - - +
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Residues in contact with PRO 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASP 3.9 1.3 - - - +
19A ASP* 1.4 84.9 - - - +
21A PHE* 1.3 63.4 + - - +
22A TYR 3.0 1.8 - - - -
23A THR* 2.6 37.4 + - + +
38A GLN* 5.0 2.9 + - - -
58A GLN* 3.9 5.0 + - - -
333B PRO* 3.5 22.9 - - + -
362B PRO 3.7 13.7 - - - +
363B ILE* 4.2 32.1 - - + -
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Residues in contact with PHE 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ASP* 3.2 16.5 + - - +
20A PRO* 1.3 77.9 - - - +
22A TYR* 1.3 57.8 + + + +
23A THR 3.4 0.2 + - - -
38A GLN* 3.7 38.5 - - + +
39A SER* 4.2 6.7 - - - -
40A ARG* 3.4 54.1 - - + +
56A GLN* 3.8 25.6 - - + -
58A GLN* 2.8 50.9 + - + +
72A VAL* 3.7 23.7 - - + +
145A PHE* 3.9 3.3 - - - -
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Residues in contact with TYR 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A PRO 5.8 0.7 - - - -
16A PRO* 3.6 51.4 - - + +
19A ASP* 2.9 20.4 + - + +
21A PHE* 1.3 79.9 - + - +
23A THR* 1.3 65.8 + - - +
40A ARG* 3.8 19.3 - - - -
56A GLN* 3.9 7.8 + - - -
72A VAL* 4.1 11.4 - - + -
99A LEU* 4.1 21.8 - - + +
102A ALA* 4.5 6.1 - - + -
104A SER* 2.5 35.8 + - - -
105A TYR* 3.8 8.5 + + - +
141A ASP* 3.6 11.0 - - - -
145A PHE* 3.6 35.5 - + + +
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Residues in contact with THR 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ASP 4.4 2.5 - - - +
20A PRO* 2.6 35.9 + - + +
21A PHE 3.3 1.0 + - - -
22A TYR* 1.3 83.6 - - - +
24A THR* 1.3 63.9 + - - +
25A PRO* 3.7 2.4 - - - +
58A GLN* 3.1 21.1 + - - -
70A ALA* 4.1 0.2 - - - +
145A PHE* 3.4 11.7 - - - -
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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