Contacts of the helix formed by residues 288 - 303 (chain A) in PDB entry 2IL1
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 ASN 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A CYS* 4.0 6.9 - - - +
280A GLU 2.8 27.3 + - - +
281A ALA* 3.9 5.2 - - + -
286A ASN 4.0 2.0 + - - -
287A PHE* 1.3 95.2 - - - +
289A VAL* 1.3 61.7 + - - +
291A GLU* 3.2 28.2 + - - +
292A ILE* 3.1 26.7 + - - +
1401A UNX 3.7 20.7 - - - -
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 3.7 34.3 - - + +
157A ARG* 3.9 9.0 - - + -
158A PHE* 3.8 21.3 - - + +
282A SER 3.5 24.5 - - - +
283A ALA* 3.8 14.1 - - - -
286A ASN* 3.5 23.4 + - - +
287A PHE 3.1 5.1 - - - +
288A ASN* 1.3 75.1 - - - +
290A ASP* 1.3 68.1 + - - +
291A GLU* 3.5 0.8 + - - -
292A ILE* 3.2 22.3 - - - +
293A PHE* 3.3 13.5 - - + -
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Residues in contact with ASP 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PHE* 3.7 26.1 - - + -
178A LYS* 5.7 0.7 + - - -
286A ASN* 4.2 15.2 + - - +
289A VAL* 1.3 76.2 - - - +
291A GLU* 1.3 66.3 + - - +
293A PHE* 3.3 5.0 + - - +
294A LEU* 2.8 46.4 + - + +
501A CA 2.2 28.4 - - - -
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Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ASN* 3.2 39.8 + - - +
289A VAL 3.2 0.4 - - - -
290A ASP* 1.3 82.2 + - - +
292A ILE* 1.3 61.1 + - - +
294A LEU* 4.4 9.6 - - + +
295A LYS* 2.9 37.0 + - + +
501A CA 2.5 31.1 - - - -
1401A UNX 4.0 9.4 - - - -
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Residues in contact with ILE 292 (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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154A LEU* 3.8 39.5 - - + -
215A ILE* 4.5 12.4 - - + +
247A LEU* 3.8 20.5 - - + +
249A VAL* 3.8 22.0 - - + -
279A CYS* 3.3 34.5 - - - -
281A ALA* 4.7 2.5 - - + -
288A ASN 3.1 13.1 + - - +
289A VAL 3.2 17.7 - - - +
291A GLU* 1.3 76.7 - - - +
293A PHE* 1.3 76.2 + - + +
296A LEU* 3.3 22.5 + - - +
1401A UNX 4.2 0.2 - - - -
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Residues in contact with PHE 293 (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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141A VAL* 4.5 6.7 - - + -
143A ILE* 3.8 18.6 - - + -
154A LEU* 3.9 9.0 - - + -
155A MET* 4.1 12.8 - - - -
158A PHE* 3.4 47.8 - + + -
189A LEU* 4.4 7.0 - - + -
191A ILE* 3.8 37.7 - - + -
215A ILE* 3.5 25.8 - - + -
289A VAL* 3.3 22.7 - - + -
290A ASP 3.3 2.7 + - - +
292A ILE* 1.3 88.4 - - + +
294A LEU* 1.3 61.3 + - - +
296A LEU* 3.5 4.6 + - - +
297A VAL* 2.9 36.0 + - - +
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Residues in contact with LEU 294 (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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158A PHE* 4.6 8.5 - - + -
180A VAL* 4.2 32.8 - - + -
181A GLU 5.1 4.7 - - - +
182A LEU* 3.9 29.0 - - + +
189A LEU* 6.4 0.2 - - + -
290A ASP* 2.8 41.4 + - + +
291A GLU* 4.3 7.2 - - + +
293A PHE* 1.3 73.4 - - - +
295A LYS* 1.3 57.9 + - - +
297A VAL* 3.5 5.8 + - + +
298A ASP* 3.0 28.1 + - - +
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Residues in contact with LYS 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LEU* 4.5 3.8 - - + -
277A ARG* 3.4 54.1 - - - +
291A GLU* 2.9 24.2 + - + +
292A ILE 4.4 1.3 - - - +
294A LEU* 1.3 70.3 - - - +
296A LEU* 1.3 60.3 + - - +
298A ASP* 3.1 24.3 + - + +
299A ASP* 2.9 34.6 + - - -
302A LYS* 6.0 0.4 - - - +
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Residues in contact with LEU 296 (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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141A VAL* 4.1 11.7 - - + -
213A GLY* 3.8 10.8 - - - -
214A ILE 3.8 17.3 - - - +
215A ILE* 3.5 33.9 - - + -
245A GLU* 3.6 42.2 - - + +
246A LEU 4.2 12.1 - - - +
247A LEU* 4.3 10.6 - - + +
292A ILE 3.3 17.6 + - - +
293A PHE* 3.7 3.8 - - - +
295A LYS* 1.3 78.2 - - - +
297A VAL* 1.3 62.9 + - + +
299A ASP* 3.3 11.1 + - + +
300A ILE* 3.0 29.1 + - + +
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Residues in contact with VAL 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 3.9 14.8 - - + -
141A VAL* 5.2 5.4 - - + -
180A VAL* 4.8 8.7 - - + -
182A LEU* 3.8 18.4 - - + -
187A ILE* 4.3 13.0 - - + -
189A LEU* 3.8 36.3 - - + -
293A PHE 2.9 24.4 + - - +
294A LEU* 3.7 6.7 - - + +
296A LEU* 1.3 74.1 - - - +
298A ASP* 1.3 56.8 + - - +
300A ILE* 3.2 9.5 + - - +
301A LEU* 3.0 39.3 + - + +
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Residues in contact with ASP 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LEU* 4.1 14.1 - - + +
183A ARG* 3.6 26.4 - - - -
294A LEU 3.0 14.1 + - - +
295A LYS* 3.1 32.9 + - + +
297A VAL* 1.3 77.8 - - - +
299A ASP* 1.3 64.3 + - - +
301A LEU* 3.4 4.8 + - - +
302A LYS* 3.1 56.4 + - - +
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Residues in contact with ASP 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLU* 3.8 26.3 - - + +
246A LEU 5.3 1.7 - - - +
247A LEU* 5.6 0.3 - - - +
275A GLY 5.4 2.6 - - - +
277A ARG* 3.0 46.9 + - - +
295A LYS* 2.9 19.6 + - - +
296A LEU* 3.4 14.2 - - - +
298A ASP* 1.3 79.0 - - - +
300A ILE* 1.3 63.4 + - - +
302A LYS* 3.6 13.9 + - - +
303A LYS* 3.6 23.9 + - - +
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Residues in contact with ILE 300 (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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139A LEU* 4.2 18.8 - - + -
141A VAL* 4.1 15.9 - - + -
212A LYS* 3.6 48.5 - - + +
213A GLY* 3.7 9.2 - - - +
245A GLU* 4.0 14.4 - - + -
296A LEU* 3.0 24.5 + - + +
297A VAL* 3.2 10.7 + - - +
299A ASP* 1.3 73.7 - - - +
301A LEU* 1.3 64.2 + - - +
303A LYS* 3.1 16.0 + - - +
304A MET* 3.5 33.5 + - + +
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Residues in contact with LEU 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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137A PHE* 3.6 40.2 - - + -
139A LEU* 4.2 13.0 - - + -
182A LEU* 3.8 25.4 - - + +
183A ARG* 6.3 1.1 - - - -
185A LYS* 5.2 7.0 - - + -
187A ILE* 3.8 19.7 - - + -
297A VAL* 3.0 24.7 + - + +
298A ASP* 3.9 5.4 - - - +
300A ILE* 1.3 75.0 - - - +
302A LYS* 1.3 61.4 + - + +
304A MET* 3.4 32.9 - - - +
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Residues in contact with LYS 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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183A ARG* 5.3 4.8 - - - +
295A LYS* 6.0 0.7 - - - +
298A ASP* 3.1 50.8 + - - +
299A ASP* 3.7 15.3 - - - +
300A ILE 3.2 0.4 - - - -
301A LEU* 1.3 76.2 - - - +
303A LYS* 1.3 63.4 + - + +
304A MET 3.3 7.0 + - - +
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Residues in contact with LYS 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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243A ASP 5.9 2.0 - - - +
245A GLU* 4.0 20.2 - - + +
299A ASP 3.6 12.8 + - - +
300A ILE* 3.1 10.5 + - - +
302A LYS* 1.3 78.7 - - + +
304A MET* 1.3 58.4 + - - +
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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