Contacts of the helix formed by residues 297 - 311 (chain A) in PDB entry 6M0X
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 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A LYS 3.7 1.0 + - - -
296A LEU* 1.3 77.2 - - - +
298A LYS* 1.3 67.6 + - - +
299A GLU* 3.8 7.0 + - - +
300A GLN* 2.9 47.4 + - - +
301A LYS* 3.3 15.2 + - - +
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Residues in contact with LYS 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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297A SER* 1.3 75.5 - - - +
299A GLU* 1.3 67.0 + - + +
301A LYS* 3.1 13.3 + - - +
302A ASN* 2.6 30.3 + - - +
440A TYR* 3.2 38.4 + - + +
441A GLU* 3.4 41.3 + - - +
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Residues in contact with GLU 299 (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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297A SER* 3.3 6.8 + - - +
298A LYS* 1.3 83.2 - - + +
300A GLN* 1.3 66.2 + - + +
301A LYS 2.7 2.6 + - - -
302A ASN* 2.8 16.7 + - + +
303A GLN* 2.7 31.5 + - - +
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Residues in contact with GLN 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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289A VAL* 5.8 0.4 - - - +
291A THR* 5.0 23.4 - - - +
295A LYS 4.6 1.6 - - - +
296A LEU* 3.6 30.2 - - + +
297A SER* 2.9 52.8 + - - +
299A GLU* 1.3 75.6 - - + +
301A LYS* 1.3 57.9 + - - +
303A GLN* 3.3 19.6 - - - +
304A ILE* 3.1 25.3 - - - +
327A LEU* 5.9 5.3 - - - +
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Residues in contact with LYS 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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281A LEU* 5.1 5.4 - - + -
284A LEU* 4.2 21.5 - - + -
285A ASN* 3.3 25.0 - - - +
296A LEU* 3.8 23.3 + - + -
297A SER 3.3 14.8 - - - +
298A LYS* 3.7 11.5 - - - +
299A GLU 2.7 5.5 + - - -
300A GLN* 1.3 70.5 - - - +
302A ASN* 1.3 59.9 + - - +
303A GLN 3.0 1.8 - - - -
304A ILE* 2.9 10.5 + - - +
305A ILE* 2.8 32.8 + - + +
439A LEU 2.7 27.3 + - - +
440A TYR* 2.9 35.3 + - + -
441A GLU 4.9 0.2 - - - -
442A THR 3.3 12.3 + - - -
443A SER* 4.4 0.8 - - - +
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Residues in contact with ASN 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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298A LYS* 2.6 39.9 - - - +
299A GLU* 2.8 13.9 + - + +
301A LYS* 1.3 71.8 - - - +
303A GLN* 1.3 66.4 + - - +
305A ILE* 4.2 8.3 - - - -
306A ASN* 3.0 36.4 + - - +
440A TYR* 3.6 30.7 + - - -
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Residues in contact with GLN 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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299A GLU* 2.7 48.8 + - - +
300A GLN* 3.3 22.4 - - - +
301A LYS 3.0 0.8 - - - -
302A ASN* 1.3 82.1 - - - +
304A ILE* 1.3 60.5 + - + +
306A ASN* 3.7 3.0 - - - +
307A TYR* 2.8 31.3 + - - +
322A TYR* 4.3 13.5 + - + +
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Residues in contact with ILE 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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280A LEU* 5.7 2.2 - - + -
284A LEU* 4.5 24.2 - - + -
296A LEU* 4.7 13.7 - - + -
300A GLN 3.1 22.4 - - - +
301A LYS 2.9 7.4 + - - +
303A GLN* 1.3 74.6 - - + +
305A ILE* 1.3 57.5 + - - +
307A TYR* 4.2 4.9 - - - -
308A VAL* 2.8 41.0 + - + +
319A LEU* 4.2 20.9 - - + -
322A TYR* 4.5 13.7 - - + -
323A ILE* 3.6 45.3 - - + -
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Residues in contact with ILE 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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273A TYR* 5.1 1.8 - - - +
277A GLU* 4.4 7.4 - - + +
280A LEU* 5.0 6.3 - - + -
281A LEU* 3.3 28.0 - - + -
284A LEU* 4.9 8.5 - - + -
301A LYS 2.8 18.8 + - - +
302A ASN* 4.0 5.4 - - - +
304A ILE* 1.3 75.6 - - - +
306A ASN* 1.3 62.5 + - - +
308A VAL* 3.2 8.7 - - - +
309A LYS* 2.8 54.4 + - - +
350A PHE* 4.4 17.7 - - + -
440A TYR* 2.9 33.9 - - + +
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Residues in contact with ASN 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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302A ASN* 3.0 32.7 + - - +
303A GLN* 3.8 3.1 - - - +
305A ILE* 1.3 82.2 - - - +
307A TYR* 1.3 63.7 + - - +
309A LYS* 3.2 11.2 + - - +
310A ASN* 2.6 41.4 + - - +
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Residues in contact with TYR 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 GLN 2.8 21.8 + - - +
304A ILE* 3.6 2.5 - - + +
306A ASN* 1.3 74.0 - - - +
308A VAL* 1.3 73.4 + - + +
310A ASN* 4.0 1.3 - - - +
311A GLU* 3.1 44.9 + - - +
314A MET* 3.5 17.0 - - + -
318A LYS* 2.4 36.7 + - - +
319A LEU* 4.7 2.0 - - - -
322A TYR* 3.3 67.6 - + + +
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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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280A LEU* 4.3 16.8 - - + -
304A ILE* 2.8 24.9 + - + +
305A ILE* 3.2 11.4 - - - +
307A TYR* 1.3 80.6 - - + +
309A LYS* 1.3 69.4 + - - +
311A GLU* 3.2 16.9 - - - +
314A MET* 3.6 30.4 - - + +
319A LEU* 3.4 30.3 - - + -
349A THR 5.0 3.6 - - - +
350A PHE* 4.3 15.3 - - + -
354A ARG* 3.8 12.7 - - - -
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Residues in contact with LYS 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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273A TYR* 2.9 32.2 + - - -
305A ILE* 2.8 38.0 + - + +
306A ASN* 3.2 15.2 + - - +
308A VAL* 1.3 81.4 - - + +
310A ASN* 1.3 69.2 + - - +
311A GLU 4.2 2.8 - - - +
350A PHE* 4.3 12.6 - - + -
353A TYR* 3.4 60.6 - - + +
354A ARG* 4.4 6.4 - - - +
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Residues in contact with ASN 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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306A ASN* 2.6 41.5 + - - +
307A TYR 4.5 0.9 - - - +
309A LYS* 1.3 87.6 - - - +
311A GLU* 1.3 61.6 + - - +
312A LYS 4.0 1.0 + - - -
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Residues in contact with GLU 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 TYR* 3.1 36.1 + - + +
308A VAL 3.2 15.4 + - - +
309A LYS 3.5 1.5 - - - +
310A ASN* 1.3 79.9 - - - +
312A LYS* 1.3 68.3 + - - +
313A ALA 3.8 9.7 - - - +
314A MET* 4.6 3.9 - - + +
318A LYS* 3.1 32.6 + - - +
354A ARG* 3.8 8.8 - - - +
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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