Contacts of the helix formed by residues 21 - 31 (chain A) in PDB entry 1GN2
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 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A GLU* 3.7 15.3 - - - -
18A PRO 4.5 1.5 + - - -
20A ILE* 1.3 77.1 - - - +
22A GLY* 1.3 64.1 + - - +
23A GLN* 3.2 10.3 + - - +
24A ILE* 3.1 32.7 + - - +
25A ASN* 3.3 10.9 + - - -
168A LEU* 5.7 1.0 - - - +
169A GLN* 2.8 27.8 + - - +
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Residues in contact with GLY 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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13A TYR* 3.5 28.2 - - - +
14A GLY* 4.1 0.9 - - - -
17A GLU* 3.3 22.4 + - - -
20A ILE 3.7 0.4 + - - -
21A SER* 1.3 73.0 - - - +
23A GLN* 1.3 65.3 + - - +
25A ASN* 3.2 2.4 + - - +
26A GLU* 2.9 27.1 + - - +
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Residues in contact with GLN 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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21A SER* 3.2 7.9 + - - +
22A GLY* 1.3 75.5 - - - +
24A ILE* 1.3 64.4 + - - +
26A GLU* 3.7 12.8 - - - +
27A LEU* 3.1 36.2 + - + +
168A LEU* 3.9 23.9 - - + +
171B LYS* 4.1 27.7 - - - +
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Residues in contact with ILE 24 (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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20A ILE* 4.1 14.6 - - + -
21A SER* 3.1 19.1 + - - +
22A GLY 3.1 1.0 - - - -
23A GLN* 1.3 77.2 - - - +
25A ASN* 1.3 58.4 + - - +
26A GLU 2.9 0.9 + - - -
27A LEU* 3.0 4.7 + - - +
28A HIS* 2.8 42.9 + - + +
164A HIS 4.2 14.8 - - - +
165A ALA* 3.9 16.8 - - - +
166A PHE* 4.0 23.3 - - - -
168A LEU* 4.2 23.1 - - + +
169A GLN* 3.8 35.9 - - + +
170A TYR* 5.5 1.1 - - + -
177A PHE* 6.3 0.2 - - + -
167B TYR* 6.1 0.9 - - + -
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Residues in contact with ASN 25 (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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11A TRP* 4.0 8.2 - - + -
13A TYR* 3.0 41.0 + - + +
16A LEU* 3.4 30.3 - - - +
20A ILE* 3.5 27.3 + - - +
21A SER 3.3 4.0 + - - +
22A GLY 3.2 4.4 + - - +
24A ILE* 1.3 78.9 - - - +
26A GLU* 1.3 57.2 + - - +
28A HIS* 3.8 7.3 + - - +
29A HIS* 3.0 32.6 + - - +
79A TRP* 5.3 1.9 + - - -
80A TRP* 3.9 16.7 - - + -
83A LEU* 5.2 1.0 - - - +
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Residues in contact with GLU 26 (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 TYR* 3.6 35.6 - - + +
22A GLY 2.9 17.6 + - - +
23A GLN* 3.7 12.4 - - - +
24A ILE 2.9 0.8 + - - -
25A ASN* 1.3 77.8 - - - +
27A LEU* 1.3 69.7 + - + +
29A HIS* 4.2 0.2 - - - +
30A SER* 2.7 38.9 + - - +
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Residues in contact with LEU 27 (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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23A GLN* 3.1 25.7 + - + +
24A ILE* 3.0 4.4 + - - +
26A GLU* 1.3 79.2 - - + +
28A HIS* 1.3 59.4 + - - +
30A SER* 4.1 0.4 - - - -
31A LYS* 2.8 47.9 + - + +
32A HIS* 3.1 6.0 + - - -
168A LEU* 3.7 27.8 - - + -
167B TYR* 3.8 17.7 - - + +
171B LYS* 3.8 24.2 - - + -
172B ASN* 3.2 26.2 - - - +
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Residues in contact with HIS 28 (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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24A ILE* 2.8 30.4 + - + +
25A ASN* 3.8 1.6 + - - +
27A LEU* 1.3 80.0 - - - +
29A HIS* 1.3 56.4 + - - +
32A HIS* 3.3 15.3 - + + +
33A HIS* 2.9 28.6 + - - +
76A HIS* 3.0 15.5 + + - -
79A TRP* 3.5 23.7 + + - -
80A TRP* 3.6 19.0 - + + -
160A ASP* 2.9 19.0 + - - -
164A HIS* 3.0 22.9 + + - +
165A ALA* 4.3 6.9 - - + +
999A FE 2.4 25.5 - - - -
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Residues in contact with HIS 29 (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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6A LEU* 3.8 28.3 - - + +
7A PRO 2.9 27.7 + - - -
8A ASP* 5.0 4.3 - - - -
9A LEU* 3.4 34.3 - - + +
13A TYR* 2.9 28.5 + + + -
25A ASN 3.0 19.0 + - - +
28A HIS* 1.3 76.8 - - - +
30A SER* 1.3 61.6 + - - +
33A HIS* 3.3 20.2 - - - +
34A ALA 3.3 7.1 + - - -
80A TRP* 3.5 26.7 - + + -
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Residues in contact with SER 30 (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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6A LEU* 4.9 4.3 - - - -
13A TYR* 4.1 11.9 - - - -
26A GLU* 2.7 28.7 + - - +
27A LEU* 4.1 0.5 - - - -
29A HIS* 1.3 81.3 - - - +
31A LYS* 1.3 80.5 + - - +
34A ALA* 3.5 16.4 - - - +
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Residues in contact with LYS 31 (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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27A LEU* 2.8 33.0 + - + +
29A HIS 3.3 0.2 - - - -
30A SER* 1.3 92.0 + - - +
32A HIS* 1.3 64.0 + - - +
34A ALA* 3.9 1.7 - - - +
35A THR* 2.8 30.9 + - - -
172B ASN* 3.6 45.1 - - + +
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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