Contacts of the helix formed by residues 297 - 311 (chain A) in PDB entry 3NO1
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 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ALA* 3.3 13.4 - - - +
126A ASN* 3.6 2.7 - - - -
127A THR* 4.4 0.4 - - - -
292A SER* 2.8 28.9 + - - -
295A SER 3.6 0.6 - - - -
296A GLY* 1.3 75.6 - - - +
298A PRO* 1.3 76.8 - - - +
299A THR 3.2 3.4 - - - -
300A ALA* 3.0 13.3 + - - +
301A TRP 3.0 9.5 + - - -
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Residues in contact with PRO 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASN* 3.0 11.0 - - - +
127A THR* 3.3 26.2 - - + +
130A TRP* 3.7 12.6 - - + +
145A TRP* 3.4 40.8 - - + +
292A SER* 4.1 4.5 - - - +
297A GLY* 1.3 82.9 - - - +
299A THR* 1.3 55.7 + - - +
301A TRP* 4.2 4.0 - - + -
302A LEU* 2.8 38.3 + - - +
323A VAL* 4.1 13.7 - - + -
327A LEU* 4.0 11.2 - - + -
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Residues in contact with THR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE* 3.4 11.6 - - + +
98A GLU* 4.4 16.4 - - - +
101A TRP* 3.8 30.3 - - + -
126A ASN* 2.9 30.7 + - - +
130A TRP* 3.1 16.7 + - + +
298A PRO* 1.3 77.3 - - - +
300A ALA* 1.3 62.5 + - - +
302A LEU* 3.7 7.1 + - - +
303A ARG* 3.4 36.9 + - + +
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Residues in contact with ALA 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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101A TRP* 4.1 19.7 - - + +
272A SER* 6.3 0.4 - - - -
273A ALA* 4.5 5.2 - - + +
290A PHE* 3.9 10.5 - - + -
295A SER 3.3 26.7 - - - +
296A GLY 4.2 2.6 + - - -
297A GLY 3.0 7.8 + - - +
299A THR* 1.3 77.1 - - - +
301A TRP* 1.3 66.6 + - - +
303A ARG* 3.1 22.9 + - - +
304A THR* 3.1 14.2 + - - -
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Residues in contact with TRP 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A PHE* 2.9 50.7 + + + -
292A SER* 3.7 20.9 - - - -
297A GLY 3.0 5.5 + - - -
298A PRO* 3.7 8.3 - - + +
300A ALA* 1.3 78.4 - - - +
302A LEU* 1.3 65.3 + - + +
304A THR* 3.2 5.4 + - - -
305A ALA* 2.9 36.5 + - + -
315A MSE 3.4 39.4 - - + +
316A GLY 3.5 13.2 + - - -
317A HIS* 3.3 17.8 - + - -
327A LEU* 3.7 51.4 - - + -
328A LEU* 3.8 13.9 - - + -
331A GLN* 3.9 9.9 - - + -
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TRP* 4.7 9.4 - - + -
145A TRP* 3.5 46.2 - - + +
298A PRO 2.8 25.9 + - - +
299A THR* 4.1 4.9 - - - +
301A TRP* 1.3 88.2 - - + +
303A ARG* 1.3 65.4 + - + +
305A ALA* 3.4 5.2 + - - +
306A ALA* 3.1 21.3 + - - +
327A LEU* 4.1 9.6 - - + -
330A SER* 4.6 1.3 - - - +
331A GLN* 4.0 24.9 - - - +
306B ALA* 5.0 0.2 - - - +
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Residues in contact with ARG 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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98A GLU* 3.0 29.9 + - - +
101A TRP* 3.5 39.6 - - - -
273A ALA* 4.5 11.4 - - + -
299A THR* 3.4 22.3 + - + +
300A ALA* 3.1 13.7 + - - +
302A LEU* 1.3 74.6 - - - +
304A THR* 1.3 67.7 + - - +
306A ALA* 3.2 4.3 + - - +
307A ILE* 3.0 27.9 + - - +
306B ALA* 3.8 24.7 - - + +
309B THR* 3.5 36.4 + - - +
331B GLN* 5.9 0.2 + - - -
332B PRO* 4.3 14.6 - - - +
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Residues in contact with THR 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ALA* 3.3 25.0 - - - +
276A CYS* 3.7 26.7 - - + -
280A MSE 5.0 2.4 - - - +
288A CYS* 3.8 18.8 - - - -
290A PHE* 3.4 21.7 - - + -
300A ALA 3.1 1.4 + - - -
301A TRP 3.3 9.2 - - - -
303A ARG* 1.3 79.8 - - - +
305A ALA* 1.3 56.1 + - - +
307A ILE* 3.1 14.2 + - + +
308A ALA* 2.9 27.0 + - + +
315A MSE 4.1 11.0 - - + -
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Residues in contact with ALA 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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301A TRP* 2.9 32.9 + - + +
302A LEU* 3.4 12.8 - - - +
304A THR* 1.3 76.9 - - - +
306A ALA* 1.3 61.0 + - - +
308A ALA 3.1 8.5 + - - -
309A THR* 3.1 3.1 + - - +
315A MSE 3.9 11.9 - - + -
331A GLN* 3.8 21.8 - - - +
333A HIS* 2.8 30.2 + - - +
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Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU 3.1 11.6 + - - +
303A ARG 3.5 8.3 - - - +
305A ALA* 1.3 75.1 - - - +
307A ILE* 1.3 62.5 + - - +
309A THR* 2.7 29.4 + - - -
310A SER 3.6 1.6 + - - -
331A GLN* 5.1 1.3 + - - -
302B LEU 4.9 0.2 - - - +
303B ARG* 3.8 25.3 - - + +
306B ALA* 3.5 23.6 - - + -
307B ILE* 4.4 7.3 - - - +
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Residues in contact with ILE 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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273A ALA* 4.1 23.3 - - + +
276A CYS* 6.3 0.4 - - + -
277A ARG* 4.4 12.3 - - + -
280A MSE 3.9 10.5 - - - -
303A ARG 3.0 15.8 + - - +
304A THR* 3.4 8.7 - - + +
306A ALA* 1.3 74.8 - - - +
308A ALA* 1.3 64.1 + - - +
310A SER* 2.8 23.9 + - - +
311A TYR* 3.4 28.5 + - + -
306B ALA 4.3 2.5 - - - +
307B ILE* 3.8 33.7 - - + +
310B SER* 3.6 31.2 - - - +
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A MSE 2.9 21.3 - - + +
304A THR 2.9 12.9 + - - +
305A ALA 3.2 11.0 - - - +
307A ILE* 1.3 77.0 - - - +
309A THR* 1.3 62.6 + - - +
311A TYR 3.0 2.6 + - - -
312A ASP 3.0 17.8 + - - -
313A VAL* 3.0 28.9 + - + +
315A MSE 3.6 21.3 - - - -
333A HIS* 3.7 2.9 - - + -
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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
----------------------------------------------------------
305A ALA 3.1 6.1 + - - +
306A ALA* 2.7 19.7 + - - +
308A ALA* 1.3 75.6 - - - +
310A SER* 1.3 62.5 + - - +
312A ASP* 3.3 19.7 + - - +
313A VAL 4.9 0.4 - - - -
331A GLN* 5.2 1.3 - - - +
332A PRO* 5.0 3.4 - - + -
333A HIS* 3.3 37.7 - - + +
273B ALA* 5.5 1.4 - - - +
303B ARG* 3.6 43.2 + - - +
247D HIS* 4.1 8.1 + - - -
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Residues in contact with SER 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ALA 4.4 0.2 - - - -
307A ILE* 2.8 17.2 + - - -
309A THR* 1.3 81.1 + - - +
311A TYR* 1.3 56.0 + - - +
312A ASP 3.4 0.2 - - - -
273B ALA* 4.2 5.6 - - - -
274B SER* 2.9 38.3 + - - +
277B ARG* 2.9 29.9 + - - -
307B ILE* 3.6 24.5 - - - +
247D HIS* 5.2 0.2 - - - -
248D ASN* 3.2 17.5 - - - +
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Residues in contact with TYR 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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277A ARG* 4.2 8.2 + - + -
280A MSE 3.0 46.0 - - + -
281A GLU* 2.6 52.4 + - - +
307A ILE* 3.4 31.4 + - + -
308A ALA 3.0 2.0 + - - -
310A SER* 1.3 77.4 + - - +
312A ASP* 1.3 71.8 + - - +
313A VAL* 3.2 9.0 + - + +
277B ARG* 3.0 31.3 - - + +
311B TYR* 3.8 12.6 + - - -
248D ASN* 3.6 12.0 + - - +
251D ARG* 3.7 25.1 - - + -
252D SER* 4.4 0.5 + - - -
255D ASP* 5.8 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