Contacts of the helix formed by residues 201 - 213 (chain A) in PDB entry 5IZL
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 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A PRO 4.5 3.4 - - - -
184A VAL* 2.9 27.0 - - - +
199A PRO 4.2 0.6 + - - -
200A GLN* 1.3 75.2 - - - +
202A ILE* 1.3 63.1 + - - +
203A PRO* 3.6 8.0 - - - +
204A GLU* 4.0 13.7 + - - +
205A LEU* 3.6 11.8 + - - +
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Residues in contact with ILE 202 (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 LEU* 4.6 16.8 - - + -
26A ALA* 3.0 46.4 - - + +
27A LEU* 3.9 18.6 - - + +
30A THR* 3.4 31.6 - - + +
184A VAL* 5.0 2.7 - - + -
185A ALA 5.4 0.7 - - - +
186A ALA* 4.9 2.0 - - - -
199A PRO* 4.1 17.2 + - + +
200A GLN* 4.3 9.2 - - - +
201A GLY* 1.3 79.2 - - - +
203A PRO* 1.3 71.8 - - + +
204A GLU 3.2 1.8 - - - -
205A LEU* 3.3 4.2 + - + +
206A ILE* 3.1 24.3 + - + +
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Residues in contact with PRO 203 (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 THR* 4.5 16.6 - - + +
199A PRO 5.5 2.2 - - - +
201A GLY* 3.8 5.2 - - - +
202A ILE* 1.3 94.5 - - + +
204A GLU* 1.3 61.2 + - + +
206A ILE* 3.7 6.3 + - + +
207A GLU* 3.2 32.8 + - - +
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Residues in contact with GLU 204 (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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182A ILE* 4.1 22.2 - - + +
183A PRO* 5.2 6.9 - - - +
201A GLY* 4.0 12.5 + - - +
202A ILE 3.2 0.4 - - - -
203A PRO* 1.3 80.9 - - - +
205A LEU* 1.3 60.0 + - - +
207A GLU* 3.4 10.8 + - + +
208A LEU* 3.0 27.7 + - + +
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Residues in contact with LEU 205 (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 LEU* 4.2 26.0 - - + -
27A LEU* 4.1 20.2 - - + -
114A MET* 4.4 6.5 - - - -
142A VAL* 4.4 5.2 - - + -
144A VAL* 4.3 24.5 - - + -
182A ILE* 4.1 30.5 - - + +
184A VAL* 4.5 10.5 - - + -
201A GLY 3.6 14.5 + - - +
202A ILE* 3.3 7.4 + - + +
204A GLU* 1.3 77.8 - - - +
206A ILE* 1.3 63.4 + - - +
208A LEU* 3.4 4.9 + - + +
209A LEU* 3.1 36.1 + - + +
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Residues in contact with ILE 206 (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* 3.5 30.1 - - + +
30A THR* 4.2 6.3 - - + -
31A ALA* 3.9 30.3 - - + +
56A PHE* 3.8 25.1 - - + -
58A VAL* 4.1 14.8 - - + -
202A ILE* 3.1 25.6 + - + +
203A PRO* 4.0 6.5 - - + +
205A LEU* 1.3 77.0 - - - +
207A GLU* 1.3 57.8 + - + +
209A LEU* 4.0 6.5 - - - +
210A THR* 2.5 36.2 + - - +
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Residues in contact with GLU 207 (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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203A PRO* 3.2 21.1 + - - +
204A GLU* 3.4 9.9 + - - +
205A LEU 3.3 0.2 - - - -
206A ILE* 1.3 77.6 - - + +
208A LEU* 1.3 64.5 + - - +
210A THR* 3.5 8.6 + - - -
211A SER* 3.2 21.1 + - - -
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Residues in contact with LEU 208 (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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142A VAL* 4.7 6.5 - - + -
180A PRO* 3.5 24.2 - - + -
182A ILE* 3.4 37.7 - - + -
204A GLU* 3.0 18.0 + - + +
205A LEU* 3.8 6.7 - - + +
206A ILE 3.3 0.4 - - - -
207A GLU* 1.3 75.8 - - - +
209A LEU* 1.3 67.8 + - - +
211A SER* 2.9 17.2 + - - +
212A GLN* 2.8 34.9 + - + +
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Residues in contact with LEU 209 (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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10A VAL* 4.8 11.7 - - + -
27A LEU* 4.8 7.9 - - + -
56A PHE* 4.7 21.1 - - + -
88A VAL* 5.3 7.2 - - + -
90A LEU* 5.6 0.7 - - + -
112A LEU* 3.8 31.0 - - + -
114A MET* 4.1 28.5 - - + -
142A VAL* 4.4 9.6 - - + -
205A LEU* 3.1 29.6 + - + +
206A ILE* 4.0 5.2 - - - +
208A LEU* 1.3 77.2 - - - +
210A THR* 1.3 57.5 + - - +
212A GLN* 4.3 4.3 - - - -
213A ILE* 2.9 42.1 + - + +
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Residues in contact with THR 210 (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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56A PHE* 5.9 0.2 - - - -
58A VAL* 3.9 28.5 - - + +
59A PRO 4.5 2.0 - - - +
61A PRO* 3.7 29.2 - - + +
63A ARG* 2.4 28.8 + - - -
86A LEU* 4.4 10.9 - - + +
206A ILE* 2.5 26.8 + - - +
207A GLU* 3.6 9.1 - - - -
208A LEU 3.1 0.6 - - - -
209A LEU* 1.3 76.8 - - - +
211A SER* 1.3 51.2 + - - +
213A ILE* 4.5 4.8 - - - +
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Residues in contact with SER 211 (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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63A ARG* 3.1 19.0 + - - +
207A GLU 3.2 9.6 + - - -
208A LEU* 2.9 19.7 + - - +
210A THR* 1.3 79.1 - - - +
212A GLN* 1.3 72.4 + - - +
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Residues in contact with GLN 212 (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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112A LEU* 4.0 17.0 - - + -
140A LYS* 2.9 50.5 + - - +
141A LEU 4.9 2.4 - - - +
142A VAL* 4.4 5.8 - - + -
180A PRO* 4.0 27.8 - - + +
208A LEU* 2.8 36.3 + - + +
209A LEU* 3.9 3.6 - - - +
211A SER* 1.3 88.4 + - - +
213A ILE* 1.3 67.8 + - - +
214A SER 3.1 1.4 + - - -
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Residues in contact with ILE 213 (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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8A VAL* 3.7 34.1 - - + -
10A VAL* 3.6 30.5 - - + -
63A ARG* 2.3 43.3 + - - +
64A LEU* 4.7 9.6 - - + +
86A LEU* 4.8 14.6 - - + -
88A VAL* 4.9 5.2 - - + -
111A ASP* 5.8 0.9 - - + -
112A LEU* 3.8 20.4 - - + -
209A LEU* 2.9 29.1 + - + +
210A THR* 4.5 3.8 - - - +
211A SER 3.6 0.4 - - - -
212A GLN* 1.3 73.9 - - - +
214A SER* 1.3 62.4 + - - +
215A ILE* 4.3 5.8 - - + -
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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