Contacts of the helix formed by residues 300 - 315 (chain A) in PDB entry 2IZS
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 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A TYR* 2.9 23.2 + - + +
298A LYS 3.5 0.9 + - - +
299A PRO* 1.3 69.5 - - - +
301A TYR* 1.3 60.9 + - - +
302A ASP* 3.3 12.6 + - - +
303A TYR* 3.0 33.1 + - + +
304A LEU* 3.1 26.8 + - - +
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Residues in contact with TYR 301 (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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147A ILE* 3.7 20.2 - - + +
151A GLU* 3.6 59.5 - - + +
154A HIS* 2.7 40.3 + - + +
228A ARG* 3.5 4.5 + - - -
232A LEU* 3.9 24.9 - - + -
298A LYS* 3.9 21.1 - - - -
299A PRO* 3.1 43.8 + - + +
300A ASP* 1.3 72.4 - - - +
302A ASP* 1.3 57.8 + - - +
304A LEU* 3.3 4.2 + - - +
305A ARG* 2.9 40.5 + - - +
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Residues in contact with ASP 302 (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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151A GLU* 5.2 2.0 - - - +
300A ASP* 3.1 9.0 + - - +
301A TYR* 1.3 78.6 - - - +
303A TYR* 1.3 58.1 + - - +
305A ARG* 3.0 24.8 + - - +
306A LYS* 2.9 32.0 + - - +
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Residues in contact with TYR 303 (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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285A THR* 3.3 24.1 - - - +
289A TYR* 3.8 38.3 - + + +
300A ASP* 3.0 31.6 + - - +
302A ASP* 1.3 75.9 - - - +
304A LEU* 1.3 75.2 + - + +
306A LYS* 3.3 7.1 + - + +
307A LEU* 3.0 45.0 + - + +
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Residues in contact with LEU 304 (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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147A ILE* 3.9 17.3 - - + -
232A LEU* 3.9 21.5 - - + -
286A TYR* 3.6 28.7 - - + -
289A TYR* 3.6 28.9 - - + -
290A VAL* 3.8 21.3 - - + -
299A PRO* 4.7 0.2 - - + -
300A ASP 3.1 18.6 + - - +
301A TYR* 3.9 7.9 - - - +
302A ASP 3.3 0.2 - - - -
303A TYR* 1.3 86.9 - - + +
305A ARG* 1.3 63.5 + - - +
307A LEU* 3.4 23.3 + - + +
308A PHE* 3.4 17.8 + - - -
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Residues in contact with ARG 305 (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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144A ILE* 4.0 25.5 - - + +
147A ILE* 3.6 25.3 - - + +
148A SER* 2.9 38.8 + - - +
151A GLU* 2.9 31.9 + - - -
301A TYR* 2.9 22.6 + - - +
302A ASP* 3.0 30.1 + - - +
304A LEU* 1.3 76.0 - - - +
306A LYS* 1.3 52.0 + - - +
308A PHE* 3.0 6.9 + - - +
309A THR* 2.7 43.4 + - + +
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Residues in contact with LYS 306 (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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302A ASP 2.9 19.3 + - - +
303A TYR* 3.7 6.5 - - + +
304A LEU 3.2 0.2 - - - -
305A ARG* 1.3 74.5 - - - +
307A LEU* 1.3 58.2 + - - +
309A THR* 3.4 8.7 - - - +
310A ASP* 2.7 70.1 + - - +
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Residues in contact with LEU 307 (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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282A GLU* 3.6 23.7 - - + +
285A THR* 3.6 28.3 - - + -
286A TYR* 3.7 37.7 - - + +
303A TYR* 3.0 33.0 + - + +
304A LEU* 3.4 23.1 - - + +
306A LYS* 1.3 73.6 - - - +
308A PHE* 1.3 65.8 + - + +
310A ASP* 4.0 4.1 - - - +
311A LEU* 3.2 27.2 + - - +
314A ARG* 4.8 0.3 + - - -
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Residues in contact with PHE 308 (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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140A LEU* 3.8 22.6 - - + +
143A ALA* 3.8 23.8 - - + -
144A ILE* 3.9 15.7 - - + -
147A ILE* 3.5 24.2 - - + -
239A PHE* 4.0 4.0 - + - -
282A GLU* 3.9 28.5 - - + -
283A MET* 3.4 31.4 - - + -
286A TYR* 3.5 38.1 - + + -
304A LEU 3.4 3.1 + - - -
305A ARG 3.0 7.4 + - - +
307A LEU* 1.3 83.6 - - + +
309A THR* 1.3 60.6 + - - +
311A LEU* 3.4 3.0 + - + +
312A PHE* 2.8 31.0 + - - +
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Residues in contact with THR 309 (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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144A ILE* 3.5 31.9 - - + -
305A ARG* 2.7 29.7 + - + +
306A LYS* 3.4 12.8 - - - +
308A PHE* 1.3 68.2 - - - +
310A ASP* 1.3 70.4 + - - +
312A PHE* 3.5 7.5 - - + +
313A ASP* 3.0 34.1 + - - -
319A PHE* 6.1 0.7 - - + -
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Residues in contact with ASP 310 (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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306A LYS* 2.7 64.2 + - - +
307A LEU* 4.0 3.8 - - - +
309A THR* 1.3 76.5 + - - +
311A LEU* 1.3 57.2 + - - +
313A ASP* 3.7 8.2 - - - +
314A ARG* 2.9 48.6 + - - +
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Residues in contact with LEU 311 (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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136A LEU* 4.3 14.1 - - + -
140A LEU* 4.0 28.3 - - + -
280A PHE* 6.0 4.0 - - + -
281A PRO* 6.2 0.2 - - + -
282A GLU* 3.3 37.7 - - + +
283A MET* 5.7 2.9 - - + +
307A LEU 3.2 16.0 + - - +
308A PHE* 3.6 4.5 - - + +
310A ASP* 1.3 77.2 - - - +
312A PHE* 1.3 64.4 + - - +
314A ARG* 3.0 26.3 + - + +
315A LYS* 2.9 51.8 + - + +
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Residues in contact with PHE 312 (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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137A LYS* 3.8 12.8 - - + -
140A LEU* 3.6 26.9 - - + -
141A MET* 3.6 25.6 - - + -
144A ILE* 4.4 7.2 - - + -
308A PHE 2.8 22.1 + - - +
309A THR* 3.5 9.9 - - - +
311A LEU* 1.3 75.6 - - - +
313A ASP* 1.3 70.6 + - - +
315A LYS 3.4 3.1 + - - -
317A TYR* 3.1 64.5 + + + +
318A MET 3.5 16.6 - - - -
319A PHE* 3.3 37.7 - + + -
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Residues in contact with ASP 313 (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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309A THR* 3.0 25.7 + - - +
310A ASP* 3.7 9.0 - - - +
312A PHE* 1.3 85.6 - - - +
314A ARG* 1.3 66.6 + - - +
316A GLY* 3.0 14.1 + - - +
317A TYR 4.7 5.2 - - - +
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Residues in contact with ARG 314 (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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282A GLU* 2.7 38.6 + - - +
307A LEU 4.8 0.4 + - - -
310A ASP* 2.9 40.5 + - - +
311A LEU* 3.3 25.7 - - + +
313A ASP* 1.3 78.9 - - - +
315A LYS* 1.3 60.2 + - + +
316A GLY 3.2 1.0 + - - -
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Residues in contact with LYS 315 (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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136A LEU* 3.7 23.1 - - + +
279A ASN 5.8 1.4 + - - -
311A LEU* 2.9 36.4 + - + +
313A ASP 3.2 0.4 - - - -
314A ARG* 1.3 76.8 - - + +
316A GLY* 1.3 60.5 + - - +
317A TYR* 3.4 46.4 + - + +
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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