Contacts of the helix formed by residues 298 - 312 (chain A) in PDB entry 1F7U
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
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Residue Dist Surf HB Arom Phob DC
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296A GLN 3.4 3.9 + - - -
297A VAL* 1.3 73.2 - - - +
299A LYS* 1.3 71.3 + - - +
300A GLU* 3.0 20.8 + - - +
301A SER* 3.1 15.8 + - - -
302A MET* 3.1 24.2 + - - +
357A ASP* 2.8 32.3 + - - -
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Residues in contact with LYS 299 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A VAL 4.3 4.7 - - - +
298A SER* 1.3 81.9 - - - +
300A GLU* 1.3 77.3 + - - +
302A MET* 3.2 9.8 + - - +
303A LEU* 2.8 45.9 + - + +
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Residues in contact with GLU 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* 3.0 24.0 - - - +
299A LYS* 1.3 93.1 + - - +
301A SER* 1.3 52.5 - - - +
303A LEU* 3.2 8.9 + - - +
304A LYS* 2.8 37.2 + - - +
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Residues in contact with SER 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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298A SER* 3.1 12.7 + - - -
300A GLU* 1.3 77.6 - - - +
302A MET* 1.3 54.0 + - - +
304A LYS* 3.2 8.7 + - - +
305A ALA* 2.7 36.9 + - - +
353A GLY* 3.6 21.3 + - - -
356A MET* 3.6 17.5 - - - +
357A ASP* 2.5 32.5 + - - -
360A GLU* 6.1 0.3 - - - +
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Residues in contact with MET 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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297A VAL* 3.4 32.3 - - + +
298A SER 3.1 17.2 + - - +
299A LYS* 3.2 11.3 + - - +
301A SER* 1.3 76.5 - - - +
303A LEU* 1.3 64.3 + - + +
305A ALA* 3.3 7.8 + - - +
306A ILE* 3.1 30.3 + - + +
345A THR* 3.5 34.1 - - + +
349A THR* 3.8 29.4 - - - +
350A ARG* 4.6 5.6 - - + -
353A GLY* 4.3 4.7 - - - -
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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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299A LYS* 2.8 34.1 + - + +
300A GLU* 3.6 7.4 - - - +
302A MET* 1.3 72.6 - - + +
304A LYS* 1.3 66.2 + - - +
306A ILE* 3.0 13.7 + - + +
307A ASP* 3.0 21.8 + - - +
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Residues in contact with LYS 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 GLU 2.8 21.5 + - - +
301A SER* 3.6 5.8 - - - +
303A LEU* 1.3 73.4 - - - +
305A ALA* 1.3 58.7 + - - +
307A ASP* 3.2 10.1 + - - +
308A LEU* 2.9 45.2 + - + +
356A MET* 3.6 19.8 - - + +
360A GLU* 5.2 7.1 + - - -
391A PHE* 4.4 14.0 - - - -
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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 SER 2.7 21.0 + - - +
302A MET* 3.4 9.2 - - - +
303A LEU 3.2 0.2 - - - -
304A LYS* 1.3 73.5 - - - +
306A ILE* 1.3 57.2 + - + +
308A LEU* 3.4 1.4 + - - +
309A PHE* 2.9 50.7 + - + -
349A THR 6.0 0.7 - - - +
352A VAL* 4.3 5.8 - - + -
353A GLY* 5.3 2.5 - - - -
356A MET* 3.8 15.9 - - - +
389A MET* 3.7 17.0 - - + -
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Residues in contact with ILE 306 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A MET* 3.1 19.7 + - + +
303A LEU* 3.0 16.1 + - + +
305A ALA* 1.3 77.0 - - + +
307A ASP* 1.3 63.5 + - - +
309A PHE* 3.2 31.9 + - + +
310A LYS* 3.3 38.8 + - - +
322A VAL* 6.5 0.4 - - + -
338A VAL* 6.1 3.1 - - + +
339A GLN* 5.7 9.9 - - + +
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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 LEU 3.0 11.5 + - - +
304A LYS* 3.2 13.7 + - - +
306A ILE* 1.3 79.0 - - - +
308A LEU* 1.3 62.1 + - - +
310A LYS* 3.2 11.2 + - - +
311A GLU* 2.8 46.8 + - - +
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Residues in contact with LEU 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 LYS* 2.9 34.7 + - + +
305A ALA 3.8 4.3 - - - +
306A ILE 3.3 0.2 - - - -
307A ASP* 1.3 78.5 - - - +
309A PHE* 1.3 67.3 + - - +
311A GLU* 4.0 26.9 - - - +
312A LYS* 2.9 34.3 + - - +
314A LEU* 4.5 0.8 - - - +
356A MET* 4.5 0.2 - - + -
389A MET* 3.6 48.2 - - + +
391A PHE* 3.6 24.2 - - + -
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Residues in contact with PHE 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 ALA* 2.9 42.6 + - + -
306A ILE* 3.2 25.8 + - + +
308A LEU* 1.3 76.2 - - - +
310A LYS* 1.3 56.6 + - + +
313A GLY* 3.1 2.6 + - - -
314A LEU* 2.7 48.2 + - + +
315A THR* 3.6 33.3 + - + +
324A ILE* 4.1 7.6 - - + -
338A VAL* 4.6 20.0 - - + -
349A THR* 6.0 6.3 - - - -
352A VAL* 4.2 14.1 - - + -
385A ILE* 3.7 15.0 - - + -
389A MET* 3.4 28.0 - - - -
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Residues in contact with LYS 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 ILE* 3.5 33.7 - - + +
307A ASP* 3.2 9.6 + - - +
308A LEU 3.1 0.4 - - - -
309A PHE* 1.3 75.5 - - + +
311A GLU* 1.3 60.1 + - - +
312A LYS 2.9 2.0 - - - -
313A GLY* 2.6 24.9 + - - -
315A THR* 4.6 10.1 - - - +
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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 ASP* 2.8 40.1 + - - +
308A LEU* 3.9 22.8 - - - +
310A LYS* 1.3 72.5 - - - +
312A LYS* 1.3 76.2 + - + +
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Residues in contact with LYS 312 (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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308A LEU* 2.9 22.0 + - - +
310A LYS 2.9 0.6 - - - -
311A GLU* 1.3 101.7 + - + +
313A GLY* 1.3 65.8 - - - +
314A LEU* 3.5 24.7 - - + +
388A GLN 3.6 16.8 - - - +
389A MET* 3.7 28.0 - - - +
390A GLY* 4.6 6.3 - - - +
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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