Contacts of the helix formed by residues 294 - 303 (chain A) in PDB entry 6F3T
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 ASN 294 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A VAL* 4.9 13.3 - - - +
285A LEU* 5.3 6.3 - - + +
290A HIS 3.6 8.9 + - - +
291A MET* 3.1 14.9 + - - +
293A GLY* 1.3 77.4 - - - +
295A GLU* 1.3 63.7 + - - +
296A THR* 3.0 23.3 + - - -
297A MET* 3.0 30.8 + - + +
298A LEU* 3.1 19.2 + - - +
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Residues in contact with GLU 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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292A LYS 4.5 5.1 - - - +
293A GLY 3.9 5.4 + - - +
294A ASN* 1.3 72.7 + - - +
296A THR* 1.3 57.4 + - - +
298A LEU* 3.4 23.0 + - - +
299A ASP* 2.9 39.7 + - - +
607A ARG* 3.7 29.5 + - - +
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Residues in contact with THR 296 (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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294A ASN* 3.0 10.3 + - - -
295A GLU* 1.3 79.0 - - - +
297A MET* 1.3 71.8 + - + +
299A ASP* 3.3 4.7 + - - +
300A PHE* 3.0 21.7 + - + +
359A LEU* 3.9 27.8 - - + -
607A ARG* 4.1 4.4 + - - +
627A LEU* 2.9 34.1 + - + +
628A ALA* 4.2 10.5 - - + +
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Residues in contact with MET 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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245A VAL* 5.2 4.5 - - + -
249A LEU* 4.1 18.3 - - + +
278A ASP* 6.3 2.0 - - + -
281A VAL* 5.4 10.3 - - + -
282A LEU* 3.9 28.5 - - + -
285A LEU* 3.9 15.0 - - + -
291A MET* 4.4 16.3 - - + +
294A ASN* 3.0 36.4 + - + +
296A THR* 1.3 88.7 - - + +
298A LEU* 1.3 67.5 + - - +
300A PHE* 3.2 11.5 + - + +
301A ARG* 3.0 23.2 + - - +
359A LEU* 4.8 15.9 - - + -
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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
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253A TYR* 4.7 12.6 - - + -
291A MET* 3.6 27.4 - - + +
292A LYS* 3.4 33.9 - - + +
294A ASN 3.1 13.1 + - - +
295A GLU* 3.7 28.9 - - - +
296A THR 3.3 0.2 - - - -
297A MET* 1.3 76.4 - - - +
299A ASP* 1.3 61.6 + - - +
301A ARG* 3.4 5.0 + - + +
302A THR* 3.0 35.7 + - + +
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Residues in contact with ASP 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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295A GLU* 2.9 24.5 + - - +
296A THR 3.6 5.6 - - - +
298A LEU* 1.3 76.4 - - - +
300A PHE* 1.3 65.8 + - - +
302A THR* 3.4 6.1 + - - -
303A SER* 2.8 33.9 + - - +
607A ARG* 2.7 33.1 + - - -
626A HIS 4.8 1.4 - - - +
627A LEU* 4.2 22.1 - - + +
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Residues in contact with PHE 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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241A TYR* 4.8 9.6 - + - -
242A PRO* 4.3 6.1 - - + -
245A VAL* 3.4 39.5 - - + -
246A HIS* 3.2 47.3 + + - -
249A LEU* 4.1 9.9 - - + -
296A THR* 3.0 14.2 + - + +
297A MET* 3.2 17.7 + - + +
299A ASP* 1.3 77.1 - - - +
301A ARG* 1.3 62.9 + - - +
303A SER* 3.1 20.2 - - - +
305A PHE* 3.9 17.9 - + + -
359A LEU* 3.3 39.9 - - + -
627A LEU* 4.4 9.8 - - + +
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Residues in contact with ARG 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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207A GLN* 5.5 7.5 + - - +
246A HIS* 3.0 40.7 + - - -
249A LEU* 4.0 8.9 + - + +
250A GLU* 3.0 50.3 + - - +
253A TYR* 4.7 11.3 - - - +
254A ASN* 4.9 1.8 - - - +
291A MET* 3.5 30.1 - - + -
297A MET 3.0 15.0 + - - +
298A LEU* 3.9 5.6 - - + +
299A ASP 3.3 0.2 - - - -
300A PHE* 1.3 79.5 - - - +
302A THR* 1.3 65.9 + - + +
303A SER 3.6 1.2 + - - +
336A HIS* 3.6 40.4 + - + -
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Residues in contact with THR 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 LEU* 3.0 22.1 + - + +
299A ASP* 3.4 11.6 + - - -
301A ARG* 1.3 81.5 - - + +
303A SER* 1.3 61.0 + - - +
304A LYS* 5.8 0.7 - - - +
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Residues in contact with SER 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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246A HIS* 3.9 5.9 + - - -
299A ASP* 2.8 24.8 + - - +
300A PHE* 3.1 16.7 - - - +
301A ARG 3.3 0.7 - - - +
302A THR* 1.3 83.5 + - - +
304A LYS* 1.3 68.1 + - - +
305A PHE* 3.5 2.8 + - - +
336A HIS* 3.8 6.6 - - - +
627A LEU* 5.6 5.8 - - - +
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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