Contacts of the helix formed by residues 298 - 311 (chain A) in PDB entry 6V01
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 SER 298 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A TYR* 3.4 18.4 - - - -
296A PHE 4.1 2.1 - - - -
297A GLY* 1.3 76.2 - - - +
299A TYR* 1.3 64.6 + - - +
300A ALA* 2.9 20.6 + - - +
301A ASP* 3.4 20.2 + - - +
302A ALA* 3.7 12.6 + - - +
144J THR* 3.4 21.3 - - - -
145J ILE* 4.0 21.7 - - - +
54L ASP* 4.7 6.8 + - - -
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Residues in contact with TYR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ILE* 3.0 35.9 + - - +
277A SER 3.7 8.9 - - - -
278A TYR* 3.6 42.9 + + + +
281A TYR* 4.3 14.1 - + + -
298A SER* 1.3 75.7 + - - +
300A ALA* 1.3 60.9 + - - +
301A ASP 3.3 0.2 - - - -
302A ALA* 3.2 4.4 + - - +
303A LEU* 2.9 53.3 + - + +
141J VAL* 3.5 41.5 - - + +
144J THR* 3.8 16.3 - - + +
145J ILE* 4.7 0.6 - - + +
235J ILE* 4.6 5.4 - - + +
61L ILE* 5.0 4.9 - - + -
65L MET* 4.7 13.3 - - + +
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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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298A SER* 2.9 7.2 + - - +
299A TYR* 1.3 77.5 - - - +
301A ASP* 1.3 60.2 + - - +
303A LEU* 3.8 6.9 - - - +
304A TRP* 2.9 29.1 + - - +
323D TRP* 3.5 16.6 - - + -
145J ILE* 4.8 1.7 - - + +
57L SER* 3.5 26.2 - - - +
60L TYR* 4.3 5.0 - - + -
61L ILE* 4.1 27.4 - - + +
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Residues in contact with ASP 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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295A GLU 3.7 21.7 - - - +
296A PHE* 4.3 2.0 - - - -
297A GLY* 4.0 5.8 + - - +
298A SER* 3.4 31.0 + - - +
299A TYR 3.3 0.4 - - - -
300A ALA* 1.3 78.4 - - - +
302A ALA* 1.3 57.0 + - - +
304A TRP* 3.4 4.3 + - - +
305A TRP* 3.0 25.5 + - - +
318A LYS* 3.3 30.0 + - + +
323D TRP* 3.5 21.8 + - - -
326D LYS* 5.6 0.2 - - - -
54L ASP* 4.4 9.8 - - - +
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Residues in contact with ALA 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A SER* 2.3 37.5 + - - +
280A VAL* 5.4 1.8 - - + -
281A TYR* 3.8 23.1 - - + +
296A PHE* 3.6 27.3 - - + -
298A SER 3.7 5.8 + - - +
299A TYR* 3.2 9.4 + - - +
301A ASP* 1.3 78.5 - - - +
303A LEU* 1.3 53.2 + - - +
305A TRP* 3.3 7.3 - - - +
306A GLY 3.1 13.2 + - - -
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Residues in contact with LEU 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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273A LEU* 4.0 33.2 - - + +
274A ILE* 4.2 14.4 - - + -
277A SER* 3.5 7.6 - - - +
299A TYR* 2.9 39.5 + - + +
300A ALA* 3.8 4.9 - - - +
302A ALA* 1.3 76.7 - - - +
304A TRP* 1.3 55.2 + - - +
305A TRP 3.0 1.1 - - - -
306A GLY* 2.8 1.6 + - - -
307A VAL* 2.8 31.7 + - - +
60L TYR* 3.6 28.7 + - + +
61L ILE* 4.9 12.1 - - + -
64L VAL* 4.0 21.3 - - + -
65L MET* 5.4 1.8 - - + -
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Residues in contact with TRP 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 ALA 2.9 14.2 + - - +
301A ASP* 3.5 8.3 - - - +
303A LEU* 1.3 74.1 - - - +
305A TRP* 1.3 66.0 + - - +
307A VAL* 3.2 3.0 + - + -
308A VAL* 3.0 46.9 + - + +
315A TYR* 4.0 16.8 - + - -
317A ASP* 3.3 27.1 + - - -
318A LYS* 4.1 16.4 - - + -
319D VAL* 4.3 10.3 - - + +
320D PRO* 4.9 2.5 - - + -
323D TRP* 4.3 8.7 - + + -
326D LYS* 3.6 50.9 - - + +
329D ALA* 4.1 20.2 - - + -
330D SER* 4.5 9.0 - - - -
333D SER* 5.8 1.6 - - - -
60L TYR* 3.2 44.3 - + + -
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Residues in contact with TRP 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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277A SER* 4.0 10.8 - - - -
280A VAL* 3.8 33.4 - - + -
296A PHE* 3.9 18.8 - + + -
301A ASP 3.0 10.4 + - - +
302A ALA 3.3 15.9 - - - +
303A LEU 3.0 0.2 - - - -
304A TRP* 1.3 83.1 - - - +
306A GLY* 1.3 77.0 + - - +
308A VAL* 3.3 7.5 + - + -
309A THR* 2.9 33.7 + - + +
318A LYS* 3.6 28.7 + - + -
320A PRO* 4.1 13.1 - - + +
329A ALA* 3.7 25.8 - - + -
332A PHE* 3.5 33.9 - + - -
333A SER* 5.6 0.2 - - - -
315J TYR* 3.2 23.3 + + - -
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Residues in contact with GLY 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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273A LEU* 3.2 20.6 - - - -
277A SER* 4.2 2.0 - - - -
302A ALA 3.1 7.4 + - - -
303A LEU 2.8 9.5 + - - -
305A TRP* 1.3 91.8 - - - +
307A VAL* 1.3 61.3 + - - -
309A THR* 3.7 1.1 - - - +
310A VAL* 2.9 27.4 + - - +
332A PHE* 4.2 6.5 - - - -
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Residues in contact with VAL 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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270A PHE* 5.5 4.3 - - + -
273A LEU* 3.5 24.0 - - + +
303A LEU* 2.8 13.0 + - + +
304A TRP* 5.2 3.8 - - + -
306A GLY* 1.3 71.2 - - - +
308A VAL* 1.3 67.4 + - + +
310A VAL* 3.2 3.7 + - - +
311A THR* 3.1 34.8 + - + +
330D SER* 3.6 32.1 - - - +
333D SER* 5.2 4.7 - - - -
334D VAL* 5.1 5.6 - - + -
60L TYR* 3.3 26.9 - - + +
63L PHE* 5.8 0.4 - - + -
64L VAL* 4.7 7.2 - - + -
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Residues in contact with VAL 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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304A TRP* 3.0 38.5 + - + +
305A TRP* 3.9 8.1 - - + +
307A VAL* 1.3 83.2 - - + +
309A THR* 1.3 64.0 + - - +
311A THR 3.4 6.6 + - - -
313A ILE* 3.4 27.9 + - + +
314A GLY* 3.9 18.6 + - - +
315A TYR* 3.6 42.8 - - + +
317A ASP* 5.5 4.0 - - - +
333D SER* 6.1 1.3 - - - +
315J TYR* 5.2 4.9 - - + -
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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
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305A TRP* 2.9 33.8 + - + +
306A GLY 3.7 0.9 - - - +
308A VAL* 1.3 76.9 - - - +
310A VAL* 1.3 65.1 + - - +
311A THR 3.3 0.4 - - - -
312A THR* 3.9 3.9 + - - +
314A GLY 5.1 1.6 - - - +
332A PHE* 3.3 30.7 - - + -
333A SER* 3.9 12.1 + - - +
337A ILE* 4.2 7.8 - - - +
313J ILE* 3.5 25.6 - - - +
315J TYR* 3.2 25.2 + - - -
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Residues in contact with VAL 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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273A LEU* 4.8 5.8 - - + -
306A GLY 2.9 15.0 + - - +
307A VAL* 3.2 3.6 + - - +
309A THR* 1.3 77.6 - - - +
311A THR* 1.3 65.4 + - + +
312A THR* 3.3 1.3 - - - +
332A PHE* 3.0 45.3 - - + +
336A ALA* 3.7 17.0 - - + +
337A ILE* 4.1 13.0 - - + +
340A PHE* 2.7 62.6 - - + +
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Residues in contact with THR 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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307A VAL* 3.1 24.1 + - + +
308A VAL 3.4 0.4 + - - -
309A THR 3.3 0.2 - - - -
310A VAL* 1.3 87.3 - - + +
312A THR* 1.3 73.0 + - - +
313A ILE* 3.2 14.6 + - - +
340A PHE* 5.2 6.3 - - + -
312D THR* 4.2 3.3 - - - +
333D SER* 4.8 4.3 - - - -
334D VAL* 4.0 27.1 - - + -
337D ILE* 3.2 37.6 - - + +
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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