Contacts of the helix formed by residues 287 - 302 (chain A) in PDB entry 2NL9
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 287 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A SER* 3.5 30.5 - - - +
186A LEU* 4.0 13.1 - - + +
187A ARG* 3.9 28.7 - - + +
190A ALA* 3.7 19.7 - - + -
275A ALA* 3.7 29.2 - - + +
278A LEU* 6.0 1.8 - - + -
279A LYS* 4.5 13.2 - - + -
286A CYS* 1.3 76.8 - - - +
288A GLU* 1.3 79.7 + - - +
289A PRO* 3.5 1.1 - - - -
290A LEU* 3.2 11.4 + - - +
291A ALA* 2.9 26.4 + - + +
1005A ZN 3.8 1.2 - - - -
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Residues in contact with GLU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LEU* 3.6 15.6 - - - +
183A SER* 2.6 28.6 + - - -
187A ARG* 2.9 30.0 + - - +
286A CYS* 3.2 20.6 - - - -
287A ILE* 1.3 82.5 - - - +
289A PRO* 1.4 61.6 - - + +
291A ALA* 3.2 0.7 + - - +
292A GLU* 2.8 53.5 + - - +
1001A ZN 4.3 4.0 - - - -
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Residues in contact with PRO 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A GLU* 3.2 22.9 - - + +
241A ASP* 3.4 30.1 - - - +
243A VAL* 3.8 9.9 - - + +
286A CYS* 3.7 18.8 - - + +
287A ILE 3.7 2.7 - - - -
288A GLU* 1.4 92.8 - - + +
290A LEU* 1.3 57.1 + - - +
292A GLU* 3.7 11.5 - - - +
293A SER* 2.9 30.1 + - - -
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 4.2 9.0 - - + -
237A ILE* 4.1 14.4 - - + -
240A GLU 4.3 3.0 + - - +
243A VAL* 3.8 21.3 - - + +
246A LEU* 3.9 28.7 - - + -
271A GLY 4.1 4.7 - - - +
274A VAL* 3.8 8.3 - - + -
275A ALA* 3.8 29.8 - - + +
278A LEU* 3.3 33.0 - - + -
286A CYS 5.9 0.2 - - - +
287A ILE* 3.2 11.2 + - - +
289A PRO* 1.3 74.8 - - - +
291A ALA* 1.3 67.1 + - - +
293A SER* 3.1 3.3 + - - -
294A ILE* 3.0 29.5 + - + +
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LEU* 3.9 1.1 - - + -
182A ILE* 4.1 6.0 - - + +
183A SER* 3.2 43.7 - - - +
186A LEU* 3.8 15.6 - - + +
287A ILE* 2.9 20.1 + - + +
288A GLU* 3.2 4.9 + - - +
290A LEU* 1.3 73.8 - - - +
292A GLU* 1.3 54.9 + - - +
294A ILE* 3.4 1.8 + - - +
295A THR* 2.7 38.9 + - - -
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Residues in contact with GLU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 3.9 17.2 + - - +
179A LEU* 3.8 26.2 - - + +
288A GLU* 2.8 32.8 + - - +
289A PRO* 3.7 10.0 - - - +
291A ALA* 1.3 77.9 - - - +
293A SER* 1.3 56.6 + - - +
295A THR* 3.7 0.9 - - - -
296A ASP* 2.8 31.9 + - - +
1001A ZN 2.1 36.5 - - - -
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Residues in contact with SER 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A VAL* 3.8 37.5 + - - +
246A LEU* 5.4 1.2 - - - +
247A SER* 3.8 15.1 + - - -
250A MSE 3.9 6.9 - - - +
289A PRO 2.9 17.4 + - - -
290A LEU* 3.1 5.8 + - - -
292A GLU* 1.3 77.2 - - - +
294A ILE* 1.3 62.1 + - - +
296A ASP* 3.4 7.9 + - - +
297A VAL* 3.1 25.6 + - - +
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Residues in contact with ILE 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ILE* 4.2 9.2 - - + -
186A LEU* 4.0 19.5 - - + -
246A LEU* 4.4 9.9 - - + -
250A MSE 3.7 30.5 - - + +
267A LEU* 4.5 5.2 - - + +
268A ILE* 4.0 29.6 - - + +
271A GLY* 3.7 30.3 - - - -
290A LEU* 3.0 18.7 + - + +
291A ALA 3.7 3.4 - - - +
293A SER* 1.3 72.6 - - - +
295A THR* 1.3 66.7 + - - +
297A VAL* 3.4 2.8 + - - +
298A LEU* 3.0 31.6 + - + +
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Residues in contact with THR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 3.5 28.7 - - + -
178A SER* 3.8 14.8 - - - -
179A LEU* 3.6 36.9 - - - +
182A ILE* 3.5 21.3 - - - +
291A ALA 2.7 21.7 + - - -
292A GLU 3.8 2.7 - - - -
294A ILE* 1.3 77.9 - - - +
296A ASP* 1.3 54.3 - - - +
298A LEU* 4.5 1.8 - - - -
299A VAL* 2.7 35.6 + - + +
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Residues in contact with ASP 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 4.5 10.5 - - + -
247A SER* 4.7 3.8 + - - -
292A GLU 2.8 19.4 + - - +
293A SER* 3.4 9.0 - - - +
295A THR* 1.3 76.0 - - - +
297A VAL* 1.3 68.7 + - - +
300A ARG* 2.7 78.0 + - - +
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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
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247A SER* 3.5 24.9 - - - +
250A MSE 3.8 32.3 - - + -
251A ILE* 3.8 26.7 - - + -
254A PHE* 4.3 17.5 - - + -
293A SER 3.1 12.3 + - - +
294A ILE 3.8 6.5 - - - +
295A THR 3.3 0.2 - - - -
296A ASP* 1.3 84.2 - - - +
298A LEU* 1.3 64.0 + - + +
300A ARG* 4.9 1.1 - - - +
301A THR* 2.6 42.7 + - - +
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A SER* 6.3 0.2 - - - -
182A ILE* 3.9 22.9 - - + -
250A MSE 6.1 0.9 - - - -
254A PHE* 4.1 21.8 - - + -
264A ILE* 3.7 48.5 - - + +
267A LEU* 4.9 5.6 - - + -
268A ILE* 4.0 12.6 - - + -
294A ILE* 3.0 21.7 + - + +
295A THR* 3.8 3.8 - - - +
297A VAL* 1.3 79.4 - - + +
299A VAL* 1.3 63.5 + - + +
301A THR* 4.7 0.4 - - - -
302A LYS* 3.0 37.4 + - + +
306A LEU* 3.6 8.1 - - + +
312A TRP* 5.3 4.0 - - + -
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Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 4.3 8.5 - - + +
175A TYR* 4.1 23.6 - - + +
178A SER* 3.5 35.2 - - - +
295A THR* 2.7 27.8 + - + +
296A ASP* 5.3 0.2 - - - -
298A LEU* 1.3 75.1 - - + +
300A ARG* 1.3 60.0 + - - +
303A ARG* 3.0 67.5 + - - +
306A LEU* 3.9 12.6 - - + -
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Residues in contact with ARG 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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247A SER* 5.4 2.0 + - - -
251A ILE* 5.0 1.2 - - - +
296A ASP* 2.7 55.7 + - - +
297A VAL* 4.7 5.3 - - - +
299A VAL* 1.3 80.6 - - - +
301A THR* 1.3 76.3 + - - +
303A ARG* 3.8 15.5 + - - +
2001A CL 3.4 31.3 - - - +
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Residues in contact with THR 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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251A ILE* 3.8 26.3 - - + +
254A PHE* 5.0 1.4 - - - -
297A VAL* 2.6 30.4 + - - +
300A ARG* 1.3 105.8 - - - +
302A LYS* 1.3 81.3 + - - +
303A ARG 3.6 0.2 - - - -
2001A CL 4.0 4.9 - - + -
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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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254A PHE* 3.8 42.5 + - + +
257A GLY* 5.7 2.2 - - - -
258A VAL 4.9 0.4 + - - -
259A THR* 2.9 41.1 + - + +
264A ILE* 5.4 2.2 - - + -
297A VAL 4.7 0.4 - - - +
298A LEU* 3.0 25.5 + - + +
301A THR* 1.3 96.7 + - - +
303A ARG* 1.3 66.3 + - - +
304A ASP 3.4 1.8 - - - -
305A TRP* 3.0 25.6 + - + -
306A LEU* 2.8 24.3 + - + +
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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
------------------------------------------------------------
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