Contacts of the helix formed by residues 21 - 36 (chain G) in PDB entry 4GEK
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 ASP 21 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G THR* 3.0 32.3 + - + +
20G PHE* 1.3 74.6 - - - +
22G GLU* 1.3 61.2 + - - +
23G ARG* 3.3 19.6 + - - +
24G VAL* 3.0 26.4 + - - +
25G ALA* 2.9 24.1 + - - +
93G ALA* 3.4 10.7 - - - +
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Residues in contact with GLU 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G ASP* 1.3 76.0 - - - +
23G ARG* 1.3 57.9 + - - +
25G ALA* 3.3 5.1 + - + +
26G GLU* 2.9 29.8 + - + +
93G ALA* 3.5 14.9 - - + +
96G GLU* 3.8 24.9 - - - +
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Residues in contact with ARG 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ASP* 3.1 18.4 + - - +
22G GLU* 1.3 79.9 - - - +
24G VAL* 1.3 63.2 + - - +
26G GLU* 3.3 14.5 + - - +
27G VAL* 3.4 17.2 + - + +
194G GLU* 4.0 26.2 + - - +
195G ILE* 3.4 31.3 - - + +
198G LYS* 3.0 43.9 - - - +
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Residues in contact with VAL 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G TRP* 3.7 36.6 - - + -
19G THR 3.4 22.2 - - - +
20G PHE* 3.9 18.8 - - + -
21G ASP* 3.0 21.4 + - - +
23G ARG* 1.3 77.9 - - - +
25G ALA* 1.3 57.1 + - - +
27G VAL* 3.3 7.7 + - - +
28G PHE* 2.8 43.3 + - + +
31G MET* 4.7 5.2 - - + -
94G MET* 4.6 1.6 - - - -
195G ILE* 4.1 15.5 - - + -
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Residues in contact with ALA 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G ASP 2.9 14.9 + - - +
22G GLU* 3.7 10.1 - - + +
24G VAL* 1.3 78.3 - - - +
26G GLU* 1.4 52.8 + - - +
28G PHE* 3.7 2.9 + - - -
67G LEU* 3.4 19.3 - - + +
93G ALA 4.1 16.8 - - - +
94G MET* 3.6 27.5 - - - -
97G ARG* 2.8 35.0 + - + -
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Residues in contact with GLU 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G GLU* 2.9 15.3 + - + +
23G ARG* 3.6 10.5 - - - +
24G VAL 3.2 0.2 - - - -
25G ALA* 1.4 76.5 - - - +
27G VAL* 1.3 63.6 + - + +
29G PRO* 3.8 2.9 - - - +
97G ARG* 3.0 28.3 + - - +
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Residues in contact with VAL 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G ARG* 3.5 16.8 - - + +
24G VAL* 3.6 9.4 - - - +
26G GLU* 1.3 79.9 - - + +
28G PHE* 1.3 67.9 + - - +
29G PRO* 3.3 3.4 - - - -
30G ASP* 3.0 12.6 + - + +
31G MET* 2.9 28.9 + - + +
193G LEU* 4.1 31.0 - - + -
194G GLU 6.2 0.2 - - - +
195G ILE* 4.1 26.5 - - + +
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Residues in contact with PHE 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G PHE* 4.5 2.9 - + - -
24G VAL* 2.8 21.8 + - + +
25G ALA* 3.8 10.1 - - - +
26G GLU 3.3 0.4 - - - -
27G VAL* 1.3 77.7 - - - +
29G PRO* 1.3 74.9 - - + +
31G MET* 3.6 19.4 - - + +
32G ILE* 2.9 59.4 + - + +
39G TYR* 4.9 2.2 - - - -
66G SER* 3.6 31.0 - - - -
67G LEU* 4.0 12.6 - - + -
69G ALA* 6.3 0.2 - - + -
94G MET* 3.9 14.6 - - + -
303G GEK 3.6 47.3 - - + -
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Residues in contact with PRO 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G GLU 3.8 11.0 - - - +
27G VAL 3.4 4.9 - - - +
28G PHE* 1.3 98.7 - - + +
30G ASP* 1.3 58.5 + - - +
32G ILE* 3.9 3.9 - - + +
33G GLN* 3.0 30.1 + - - +
39G TYR* 5.9 2.7 - - + -
67G LEU* 3.9 15.7 - - + -
97G ARG* 3.9 13.9 - - - +
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Residues in contact with ASP 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G VAL* 3.0 17.3 + - + +
29G PRO* 1.3 79.8 - - - +
31G MET* 1.4 56.8 + - - +
33G GLN* 3.1 10.8 + - - +
34G ARG* 2.9 76.3 + - - +
193G LEU* 4.1 9.2 - - - +
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Residues in contact with MET 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G TRP* 4.0 17.0 - - + -
24G VAL* 4.7 4.7 - - + -
27G VAL* 2.9 24.0 + - + +
28G PHE* 3.6 33.4 - - + +
30G ASP* 1.4 75.1 - - - +
32G ILE* 1.3 67.3 + - + +
34G ARG* 3.4 1.7 + - - +
35G SER* 2.8 29.1 + - - +
190G TYR* 4.7 2.9 - - + -
193G LEU* 3.5 18.9 - - + +
195G ILE* 3.7 27.1 - - + -
199G ARG* 3.6 50.0 - - + +
303G GEK 5.0 0.2 - - - +
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Residues in contact with ILE 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G PHE* 2.9 60.3 + - + +
29G PRO* 3.9 3.4 - - + +
31G MET* 1.3 84.1 - - + +
33G GLN* 1.3 68.4 + - - +
35G SER* 4.0 1.8 - - - -
36G VAL* 2.9 34.2 + - + +
39G TYR* 3.3 48.2 - - + -
133G PHE* 6.4 0.2 - - + -
199G ARG* 3.9 21.3 - - - +
303G GEK 4.1 7.2 - - + +
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Residues in contact with GLN 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G PRO 3.0 18.9 + - - +
30G ASP* 3.1 12.6 + - - +
32G ILE* 1.3 81.7 - - - +
34G ARG* 1.3 64.4 + - + +
35G SER 3.4 0.5 + - - -
36G VAL 4.3 3.3 + - - +
39G TYR* 5.3 8.4 - - + -
40G SER* 4.5 18.0 + - - -
184G PHE* 3.9 17.3 - - - -
188G ASN* 4.9 7.3 - - - +
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Residues in contact with ARG 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G ASP* 2.9 51.4 + - - +
31G MET 4.1 3.4 - - - +
32G ILE 3.2 0.4 - - - -
33G GLN* 1.3 80.2 - - + +
35G SER* 1.3 58.5 + - - +
184G PHE* 3.6 10.1 - - - -
185G LYS* 3.6 23.2 - - - +
188G ASN* 3.2 31.9 + - + +
189G GLY* 2.9 35.1 + - - -
190G TYR* 3.9 18.2 - - + +
192G GLU* 2.8 32.3 + - - +
193G LEU* 4.0 18.0 - - + +
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Residues in contact with SER 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G MET* 2.8 21.3 + - - +
32G ILE* 3.1 2.5 + - - -
34G ARG* 1.3 81.1 - - - +
36G VAL* 1.3 70.0 + - - +
37G PRO* 3.4 2.9 - - - +
181G HIS* 2.7 29.0 + - - -
184G PHE* 4.2 2.2 - - - -
185G LYS* 4.2 8.7 - - - -
190G TYR* 3.6 24.4 - - - -
199G ARG* 4.0 13.2 + - - -
203G GLU* 4.4 11.0 - - - +
235G PHE* 3.9 2.3 - - - -
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Residues in contact with VAL 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G ILE* 2.9 29.4 + - + +
33G GLN 4.4 2.3 - - - +
34G ARG 3.9 0.8 - - - -
35G SER* 1.3 84.0 - - - +
37G PRO* 1.3 70.2 - - - +
38G GLY 3.3 0.5 + - - -
39G TYR* 3.1 30.8 + - + +
133G PHE* 3.7 37.2 - - + -
184G PHE* 4.2 5.1 - - - -
199G ARG* 3.9 23.6 - - - +
235G PHE* 3.8 20.4 - - + -
303G GEK 5.6 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