Contacts of the helix formed by residues 29 - 38 (chain A) in PDB entry 3GIA
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 ILE 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ALA 2.9 23.3 + - - +
25A SER* 3.9 7.2 - - - -
28A SER* 1.3 73.9 - - - +
30A PHE* 1.3 66.3 + - - +
31A GLY 3.1 3.6 + - - -
32A VAL* 3.2 14.7 + - + +
33A GLY 3.3 0.7 + - - -
103A LEU* 3.7 31.6 - - + -
196A ILE* 4.6 3.8 - - + +
197A PHE* 3.1 55.2 - - + -
199A LEU* 3.8 24.5 - - + -
200A SER* 3.8 5.6 - - - +
340A MET* 4.0 10.5 - - + -
344A ALA* 3.7 16.8 - - + -
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Residues in contact with PHE 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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25A SER 3.2 11.2 + - - +
26A ILE* 3.2 31.2 - - + +
28A SER 3.6 2.4 - - - -
29A ILE* 1.3 76.3 - - - +
31A GLY* 1.3 63.1 + - - +
33A GLY* 3.2 3.8 + - - -
34A ALA* 3.1 20.1 + - + +
41A LEU* 3.5 31.1 - - + +
45A PHE* 4.1 18.6 - + - -
111A TYR* 5.9 0.4 - - - +
197A PHE* 4.3 4.0 - - - -
239A VAL* 4.0 12.6 - - + -
240A ALA* 3.8 25.6 - - - -
243A ALA* 4.1 10.3 - - + -
244A ILE* 5.3 0.9 - - + -
252A LEU* 4.3 15.9 - - + -
259A ALA* 4.1 14.4 - - + -
260A LEU* 3.7 26.0 - - + -
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Residues in contact with GLY 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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28A SER 4.9 2.0 + - - -
29A ILE 3.1 1.2 + - - -
30A PHE* 1.3 75.4 - - - +
32A VAL* 1.3 64.8 + - - +
34A ALA* 3.1 10.9 + - - +
35A LYS* 3.0 22.2 + - - +
252A LEU 5.1 0.7 - - - -
253A ILE* 5.1 1.9 - - - +
256A SER* 3.4 41.5 + - - -
259A ALA* 4.5 7.3 - - - +
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Residues in contact with VAL 32 (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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29A ILE* 3.2 13.1 + - + +
31A GLY* 1.3 74.1 - - - +
33A GLY* 1.3 57.9 + - - +
35A LYS* 3.3 11.3 + - + +
36A ILE* 3.0 47.1 + - + +
196A ILE* 4.4 16.2 - - + -
197A PHE* 4.5 1.8 - - + -
256A SER* 3.8 5.5 + - - +
340A MET* 3.9 20.6 - - + -
341A GLU* 3.6 46.7 - - + +
344A ALA* 5.3 0.7 - - + -
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Residues in contact with GLY 33 (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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29A ILE 3.3 4.4 + - - -
30A PHE 3.2 5.0 + - - -
31A GLY 3.1 1.0 - - - -
32A VAL* 1.3 76.9 - - - +
34A ALA* 1.3 57.3 + - - +
36A ILE 4.5 0.2 - - - -
37A ALA* 2.8 35.4 + - - +
38A GLY 3.4 2.6 + - - -
41A LEU* 3.7 13.8 - - - +
193A ALA* 5.0 4.9 - - - -
197A PHE* 3.4 27.3 - - - -
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Residues in contact with ALA 34 (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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30A PHE* 3.1 15.8 + - + +
31A GLY* 3.1 12.3 + - - +
33A GLY* 1.3 74.8 - - - +
35A LYS* 1.3 59.2 + - - +
38A GLY* 3.0 34.7 + - - +
41A LEU* 4.2 8.3 - - + +
244A ILE* 6.1 0.2 - - + -
249A ILE* 4.5 2.5 - - + +
252A LEU* 4.1 35.4 - - + +
253A ILE* 3.7 15.7 - - + +
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Residues in contact with LYS 35 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLY 3.0 11.3 + - - +
32A VAL* 3.4 14.2 - - + +
33A GLY 3.2 0.2 - - - -
34A ALA* 1.3 79.1 - - - +
36A ILE* 1.3 66.2 + - + +
38A GLY* 4.4 1.0 + - - -
253A ILE* 3.6 44.5 + - + +
256A SER* 4.7 13.7 + - - -
341A GLU* 4.5 14.6 - - - +
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Residues in contact with ILE 36 (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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32A VAL* 3.0 31.9 + - + +
35A LYS* 1.3 82.4 - - + +
37A ALA* 1.3 61.4 + - - +
38A GLY 3.6 0.2 - - - -
189A GLY* 3.3 35.5 - - - +
192A PHE* 4.4 6.3 - - + -
193A ALA* 3.8 18.6 - - + +
196A ILE* 3.4 32.3 - - + -
197A PHE* 6.1 0.2 - - + -
341A GLU* 4.0 12.8 - - - +
393A TYR* 3.5 27.1 - - + +
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Residues in contact with ALA 37 (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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33A GLY 2.8 19.5 + - - +
36A ILE* 1.3 74.2 - - - +
38A GLY* 1.3 61.8 + - - +
39A ARG* 3.2 0.9 + - - +
40A ASN* 2.9 21.8 + - - +
41A LEU* 3.8 14.1 - - + +
44A THR* 3.4 26.2 - - - +
186A ALA* 4.7 4.6 - - - +
189A GLY 4.0 6.5 - - - -
190A MET* 4.0 6.7 - - - -
193A ALA* 3.8 12.1 - - + -
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Residues in contact with GLY 38 (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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33A GLY 3.4 1.8 + - - -
34A ALA* 3.0 24.9 + - - -
35A LYS 4.4 1.2 + - - -
36A ILE 3.6 1.4 - - - -
37A ALA* 1.3 75.3 - - - +
39A ARG* 1.3 61.5 + - - -
40A ASN 3.2 0.9 + - - -
41A LEU* 3.3 18.9 + - - +
244A ILE* 3.4 7.4 - - - +
249A ILE* 3.4 19.2 - - - +
253A ILE* 5.8 0.2 - - - -
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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