Contacts of the helix formed by residues 20 - 30 (chain A) in PDB entry 3IEU
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 GLY 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ASN 3.1 3.6 - - - -
19A VAL* 1.3 79.6 - - - +
21A LYS* 1.3 63.3 + - - +
23A THR* 3.2 2.9 + - - -
24A LEU* 3.0 25.4 + - - +
95A VAL* 4.7 3.1 - - - -
124A ASN* 3.6 12.9 + - - -
156A ALA* 4.3 0.2 - - - +
302A GDP 2.9 36.0 + - - -
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Residues in contact with LYS 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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13A ILE* 3.9 29.0 - - + +
14A VAL* 3.6 24.0 - - - +
15A GLY 2.7 30.8 + - - +
16A ARG 3.1 14.1 + - - -
17A PRO* 3.7 4.0 - - - +
19A VAL* 3.7 12.9 - - + +
20A GLY* 1.3 71.4 - - - +
22A SER* 1.3 57.4 + - - +
24A LEU* 3.2 5.0 + - - +
25A LEU* 2.8 29.9 + - - +
62A ASP* 6.3 2.7 - - - -
95A VAL* 4.3 4.5 - - + -
302A GDP 2.8 39.9 + - - +
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Residues in contact with SER 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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21A LYS* 1.3 72.5 - - - +
23A THR* 1.3 62.7 + - - +
25A LEU* 3.5 10.8 - - - +
26A ASN* 3.0 32.6 + - - +
36A THR* 5.9 8.3 - - - -
302A GDP 2.5 36.5 + - - -
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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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20A GLY 3.5 7.0 - - - -
21A LYS 3.2 0.2 - - - -
22A SER* 1.3 77.4 - - - +
24A LEU* 1.3 60.3 + - - +
26A ASN* 3.4 8.0 + - - +
27A LYS* 3.2 23.2 + - + +
36A THR* 6.3 1.3 - - - -
156A ALA* 3.5 25.8 - - + +
157A GLU* 4.2 6.1 - - + +
302A GDP 2.9 52.6 + - + +
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Residues in contact with LEU 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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13A ILE* 4.6 9.6 - - + -
20A GLY 3.0 15.8 + - - +
21A LYS* 3.7 1.8 - - - +
23A THR* 1.3 74.5 - - - +
25A LEU* 1.3 66.5 + - - +
26A ASN 3.1 1.3 - - - -
27A LYS* 3.1 3.4 + - - +
28A LEU* 2.9 45.0 + - + +
93A ILE* 4.3 15.0 - - + -
95A VAL* 4.1 26.5 - - + -
122A ALA* 5.0 1.6 - - + -
124A ASN* 5.9 0.7 - - - +
154A ILE* 4.2 18.2 - - + -
156A ALA* 3.9 11.4 - - + -
162A VAL* 3.6 29.6 - - + -
165A ILE* 5.0 7.9 - - + -
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Residues in contact with LEU 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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13A ILE* 4.3 14.3 - - + +
21A LYS 2.8 16.9 + - - +
22A SER* 3.5 10.3 - - - +
24A LEU* 1.3 78.3 - - - +
26A ASN* 1.3 61.2 + - - +
28A LEU* 3.2 4.5 + - + +
29A LEU* 3.0 45.7 + - + +
48A VAL* 3.3 47.8 - - + +
49A GLY* 4.2 0.9 - - - +
60A TYR* 4.0 32.5 - - + -
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Residues in contact with ASN 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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22A SER* 3.0 21.3 + - - +
23A THR* 3.7 7.2 - - - +
24A LEU 3.1 0.2 - - - -
25A LEU* 1.3 79.6 - - - +
27A LYS* 1.3 64.1 + - - +
29A LEU* 3.3 18.4 + - - +
30A GLY* 3.2 18.4 + - - -
31A GLN 4.5 2.1 + - - +
34A SER* 3.6 35.4 + - - +
35A ILE 3.3 26.5 + - - +
36A THR* 3.8 15.2 - - - +
215A THR* 5.2 1.4 - - + +
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Residues in contact with LYS 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 THR* 3.2 11.9 + - + +
24A LEU* 3.1 9.9 + - - +
26A ASN* 1.3 75.9 - - - +
28A LEU* 1.3 63.2 + - - +
30A GLY* 3.4 9.1 + - - -
156A ALA* 3.1 28.9 - - - +
157A GLU 3.6 14.9 + - - -
158A THR 4.1 2.7 - - - -
159A GLY* 3.9 22.2 - - - +
162A VAL* 3.9 19.7 - - + +
213A SER* 3.3 26.7 + - - +
308A TRS 3.7 17.0 + - - -
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Residues in contact with LEU 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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13A ILE* 4.3 8.7 - - + -
24A LEU* 2.9 41.4 + - + +
25A LEU* 3.6 6.5 - - - +
27A LYS* 1.3 78.8 - - - +
29A LEU* 1.3 62.4 + - - +
30A GLY 3.3 0.3 + - - -
51A HIS* 3.7 18.3 + - - -
60A TYR* 3.9 40.2 - - + +
93A ILE* 4.6 1.3 - - + -
162A VAL* 4.0 17.5 - - + +
165A ILE* 4.4 12.3 - - + -
166A ALA* 3.9 35.0 - - + +
308A TRS 3.9 10.9 + - - -
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Residues in contact with LEU 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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25A LEU* 3.0 45.8 + - + +
26A ASN* 3.3 18.5 + - - +
28A LEU* 1.3 76.5 - - - +
30A GLY* 1.3 63.4 + - - +
31A GLN* 3.1 16.2 + - + +
48A VAL 5.1 0.7 - - - +
49A GLY* 4.2 8.7 - - - -
50A ILE 3.7 41.3 - - - +
51A HIS* 3.6 24.7 - - + +
60A TYR* 4.7 2.5 - - + -
308A TRS 3.9 2.1 + - - -
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Residues in contact with GLY 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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26A ASN 3.2 8.9 + - - -
27A LYS* 3.8 4.0 - - - -
28A LEU 3.1 2.8 - - - -
29A LEU* 1.3 78.3 - - - +
31A GLN* 1.3 65.0 + - - +
32A LYS 3.6 1.4 + - - -
212A TYR* 6.2 0.2 - - - -
308A TRS 3.5 34.5 + - - -
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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