Contacts of the helix formed by residues 291 - 307 (chain A) in PDB entry 5T0I
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 291 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A ASP* 5.8 1.1 - - - -
289A ALA 3.4 6.3 + - - -
290A GLY* 1.3 70.5 + - - -
292A ASP* 1.3 66.0 + - - -
293A ASN 2.9 5.2 + - - -
294A GLU* 3.1 32.3 + - - +
295A VAL* 3.8 0.5 - - - +
303B ARG* 3.0 18.7 + - - -
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Residues in contact with ASP 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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282A GLY* 4.2 12.8 - - - +
283A ALA 4.6 7.3 + - - +
284A ARG 4.0 23.4 - - - +
285A PHE* 5.2 2.2 - - - -
286A ASP* 2.9 36.9 + - - +
290A GLY* 4.1 1.6 - - - -
291A GLY* 1.3 70.6 - - - -
293A ASN* 1.3 58.9 + - - +
294A GLU 3.3 0.4 - - - -
295A VAL* 2.9 11.0 + - + +
296A GLN* 2.8 34.4 + - - +
303B ARG* 2.5 41.4 + - - +
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Residues in contact with ASN 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ARG* 4.8 4.9 + - - +
285A PHE* 4.7 18.1 - - - +
286A ASP* 4.9 10.6 + - - +
290A GLY* 3.8 20.9 + - - -
291A GLY 2.9 1.6 + - - +
292A ASP* 1.3 80.5 + - - +
294A GLU* 1.3 61.1 + - - +
296A GLN* 3.3 28.5 + - - +
297A ARG* 3.9 5.7 + - - +
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Residues in contact with GLU 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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247A GLN* 4.1 24.8 + - - +
290A GLY 5.1 3.9 - - - +
291A GLY* 3.1 28.4 + - - +
293A ASN* 1.3 77.7 - - - +
295A VAL* 1.3 68.3 + - + +
297A ARG* 3.5 33.2 + - - +
298A THR* 4.5 2.6 + - - +
300B GLY 5.6 1.4 - - - +
303B ARG* 5.7 1.2 + - - -
304B GLU* 4.6 10.7 - - - +
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Residues in contact with VAL 295 (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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279A ALA 3.9 1.3 - - - +
280A ILE* 3.3 31.7 - - - +
282A GLY* 3.9 13.5 - - - +
291A GLY 3.8 11.2 - - - +
292A ASP* 2.9 12.2 + - - +
294A GLU* 1.3 80.5 - - + +
296A GLN* 1.3 63.4 + - - +
297A ARG 3.0 2.5 - - - -
298A THR* 2.6 28.6 + - + +
299A MET* 3.4 2.8 + - - +
303B ARG* 3.3 29.4 - - - +
307B ARG* 3.4 25.8 - - - +
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Residues in contact with GLN 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLY 2.9 23.4 + - - -
283A ALA* 4.0 1.4 - - - +
284A ARG* 2.7 43.8 + - - +
292A ASP* 2.8 20.4 + - - +
293A ASN* 3.3 22.9 - - - +
294A GLU 3.2 0.4 - - - -
295A VAL* 1.3 77.7 - - - +
297A ARG* 1.3 59.6 + - - +
298A THR 3.2 0.2 - - - -
299A MET* 3.2 25.0 - - - +
300A LEU* 3.1 53.0 + - + +
301A GLU 4.0 0.3 + - - -
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Residues in contact with ARG 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 GLN* 4.6 13.2 - - - +
250A VAL* 3.3 46.1 - - + +
293A ASN 3.9 4.6 + - - +
294A GLU* 3.5 25.3 + - - +
295A VAL 3.0 0.6 - - - -
296A GLN* 1.3 78.9 - - - +
298A THR* 1.3 60.7 + - + +
301A GLU* 3.1 40.6 - - - +
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Residues in contact with THR 298 (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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242A GLY 5.9 2.0 - - - +
245A LEU* 5.5 8.5 - - + +
246A VAL* 5.9 5.2 - - + -
247A GLN* 4.8 13.5 - - - +
280A ILE* 2.5 58.7 + - + +
294A GLU 5.0 3.6 - - - +
295A VAL* 2.6 14.9 + - + +
297A ARG* 1.3 81.8 - - + +
299A MET* 1.3 60.3 + - - +
302A LEU* 3.2 27.0 + - - +
307B ARG* 5.8 2.2 - - - +
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Residues in contact with MET 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ILE* 5.7 3.1 - - + -
280A ILE* 3.4 17.7 - - + +
281A GLY* 3.4 19.1 - - - +
282A GLY 3.1 27.8 - - - +
283A ALA* 4.1 4.7 - - + -
284A ARG* 5.2 0.4 - - - -
295A VAL 3.6 13.5 - - - +
296A GLN* 3.2 23.8 - - - +
298A THR* 1.3 80.1 + - - +
300A LEU* 1.3 76.4 + - + +
302A LEU* 4.0 1.0 - - - +
303A ILE* 3.1 31.8 + - + +
328A ASP* 3.4 31.2 - - + +
329A PRO* 3.7 25.6 - - + -
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Residues in contact with LEU 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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284A ARG* 4.3 20.9 - - - +
296A GLN* 3.1 46.5 + - + +
299A MET* 1.3 82.9 - - + +
301A GLU* 1.3 58.0 + - - +
303A ILE* 3.9 4.4 - - + +
304A ASN* 2.9 30.0 + - - +
328A ASP* 3.3 27.8 - - - +
332A MET* 6.1 1.3 - - + -
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Residues in contact with GLU 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 GLY* 4.8 11.5 + - - -
253A GLY* 5.9 0.2 - - - -
254A ALA* 3.2 33.2 - - + +
296A GLN 4.0 0.2 + - - -
297A ARG* 3.1 32.3 + - - +
299A MET 3.4 0.4 - - - -
300A LEU* 1.3 76.8 - - - +
302A LEU* 1.3 58.4 + - - +
304A ASN* 3.3 8.9 + - - +
305A GLN* 2.8 46.8 + - + +
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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
----------------------------------------------------------
245A LEU* 6.1 1.8 - - + -
253A GLY 6.0 1.3 - - - +
257A VAL* 5.2 8.3 - - + -
274A PHE* 3.5 51.4 - - + -
277A ILE* 4.6 13.0 - - + -
280A ILE* 4.8 8.3 - - + -
298A THR 3.2 21.1 + - - +
299A MET 4.0 1.6 - - - +
300A LEU 3.4 0.2 - - - -
301A GLU* 1.3 79.0 - - - +
303A ILE* 1.3 58.6 + - + +
305A GLN* 3.3 5.4 + - + -
306A LEU* 2.8 49.7 + - + +
319A MET* 4.2 15.5 - - + -
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Residues in contact with ILE 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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277A ILE* 4.6 18.8 - - + -
299A MET* 3.1 21.5 + - + +
300A LEU* 4.0 5.2 - - + +
302A LEU* 1.3 76.4 - - + +
304A ASN* 1.3 58.6 + - - +
306A LEU* 3.1 20.7 + - + +
307A ASP* 2.8 51.5 + - - +
319A MET* 4.9 3.6 - - + -
329A PRO* 4.7 24.7 - - + +
332A MET* 3.9 29.4 - - + -
333A ARG* 6.0 3.4 - - + +
337A LEU* 5.7 7.6 - - + -
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Residues in contact with ASN 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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300A LEU 2.9 20.7 + - - +
301A GLU* 3.6 10.3 + - - +
303A ILE* 1.3 76.9 - - - +
305A GLN* 1.3 68.6 + - - +
307A ASP* 2.9 30.6 + - - +
308A GLY* 3.6 4.5 + - - -
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Residues in contact with GLN 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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253A GLY 5.2 0.9 - - - +
254A ALA* 4.0 12.4 + - - +
257A VAL* 3.4 39.7 - - + +
258A ARG* 3.5 25.9 - - - +
261A PHE* 5.3 0.2 - - - -
301A GLU* 2.8 34.3 + - + +
302A LEU* 3.7 6.7 - - + +
304A ASN* 1.3 86.1 + - + +
306A LEU* 1.3 61.2 + - - +
307A ASP 3.5 0.2 + - - -
308A GLY* 3.7 6.8 + - - -
312A ARG* 3.4 14.9 + - - -
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Residues in contact with LEU 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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257A VAL* 5.0 3.1 - - + -
274A PHE* 4.7 10.3 - - + -
302A LEU* 2.8 44.3 + - + +
303A ILE* 3.1 18.6 + - + +
305A GLN* 1.3 78.3 - - - +
307A ASP* 1.3 53.6 + - - +
308A GLY 3.2 6.0 + - - -
312A ARG* 3.3 29.4 - - - +
317A VAL* 4.7 11.4 - - + -
319A MET* 3.8 24.5 - - + -
336A ARG* 2.3 52.9 + - - +
337A LEU* 4.4 13.9 - - + -
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Residues in contact with ASP 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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303A ILE* 2.8 31.0 + - - +
304A ASN* 2.9 19.5 + - - +
306A LEU* 1.3 74.6 - - - +
308A GLY* 1.3 66.4 + - - +
309A PHE* 3.9 14.7 - - - -
332A MET* 3.3 29.3 - - - +
336A ARG* 3.5 28.3 - - - +
337A LEU* 5.5 0.7 - - - +
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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