Contacts of the helix formed by residues 304 - 319 (chain A) in PDB entry 1FO4
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 ALA 304 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A ALA 3.3 4.4 + - - +
303A CYS* 1.3 75.6 - - - +
305A LEU* 1.3 61.3 + - - +
306A SER* 3.8 8.7 - - - +
307A SER* 2.8 29.7 + - - +
308A VAL* 3.1 10.1 + - - +
343A LYS 3.7 7.6 - - - +
344A SER 3.6 25.6 - - - +
345A VAL* 4.4 3.4 - - - +
346A ALA 3.2 8.5 - - - +
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Residues in contact with LEU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ALA* 1.3 73.3 - - - +
306A SER* 1.3 57.6 + - - +
308A VAL* 3.2 7.9 + - + +
309A GLU* 2.8 28.8 + - - +
334A LEU* 3.9 17.1 - - + +
337A PHE* 3.3 49.1 - - + -
343A LYS* 3.2 15.4 + - + +
346A ALA* 2.9 32.0 + - + +
347A SER 4.1 2.5 - - - +
348A LEU* 4.1 31.4 - - + +
351A ASN* 5.3 0.2 - - + -
361A LEU* 3.9 20.6 - - + -
3006A FAD 4.3 2.9 - - - +
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Residues in contact with SER 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ALA* 3.8 5.9 - - - +
305A LEU* 1.3 74.7 - - - +
307A SER* 1.3 63.3 + - - +
309A GLU* 3.6 14.1 - - - +
310A LYS* 3.0 26.5 + - - +
340A LYS* 6.2 3.8 - - - -
343A LYS* 2.9 28.9 + - - +
344A SER* 3.5 19.9 + - - -
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Residues in contact with SER 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A PHE* 4.8 2.0 - - - -
303A CYS* 4.7 9.4 - - - -
304A ALA* 2.8 24.8 + - - +
306A SER* 1.3 80.6 + - - +
308A VAL* 1.3 64.5 + - - +
310A LYS* 3.2 7.4 + - - +
311A THR* 3.0 30.4 + - - -
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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
----------------------------------------------------------
299A PHE* 3.7 30.7 - - + -
303A CYS* 4.5 5.4 - - + -
304A ALA 3.1 12.7 + - - +
305A LEU* 3.4 11.4 - - + +
307A SER* 1.3 78.1 - - - +
309A GLU* 1.3 57.1 + - - +
311A THR* 3.8 1.0 - - - -
312A LEU* 2.8 52.2 + - + +
330A VAL* 4.7 2.9 - - + -
334A LEU* 4.4 8.1 - - + -
348A LEU* 3.8 35.2 - - + -
409A ILE* 4.3 7.9 - - + -
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Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LEU 2.8 16.5 + - - +
306A SER* 3.6 12.5 - - - +
308A VAL* 1.3 77.0 - - - +
310A LYS* 1.3 55.9 + - - +
313A LEU* 2.9 52.4 + - + +
331A LEU* 3.7 16.2 - - + +
334A LEU* 3.6 35.4 - - + +
335A ARG* 4.1 4.3 + - - -
340A LYS* 5.1 9.5 + - - +
343A LYS* 3.7 24.7 + - + -
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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
----------------------------------------------------------
62A GLN* 4.2 19.4 + - - +
306A SER 3.0 17.9 + - - +
307A SER* 3.2 7.8 + - - +
309A GLU* 1.3 77.9 - - - +
311A THR* 1.3 63.6 + - - +
313A LEU* 3.3 9.2 + - - +
314A GLU* 3.0 50.3 + - + +
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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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290A VAL* 4.2 13.7 - - + +
292A HIS* 4.0 29.7 - - + +
297A ILE* 4.3 4.3 - - + -
299A PHE* 3.7 29.7 - - + -
307A SER* 3.0 17.9 + - - -
310A LYS* 1.3 76.6 - - - +
312A LEU* 1.3 59.0 + - - +
314A GLU* 3.3 16.7 + - - +
315A ALA* 2.9 26.2 + - - +
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Residues in contact with LEU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ILE* 4.1 17.7 - - + -
299A PHE* 3.6 28.9 - - + -
308A VAL* 2.8 26.0 + - + +
311A THR* 1.3 73.6 - - - +
313A LEU* 1.3 60.6 + - - +
315A ALA* 3.3 3.8 + - - +
316A VAL* 2.9 34.7 + - - +
327A PHE* 3.8 30.7 - - + +
330A VAL* 3.6 37.0 - - + -
331A LEU* 3.7 18.4 - - + -
409A ILE* 3.9 9.0 - - + -
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Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLU* 2.9 41.8 + - + +
310A LYS* 3.7 8.1 - - - +
312A LEU* 1.3 74.6 - - - +
314A GLU* 1.3 64.8 + - + +
316A VAL* 3.3 4.7 + - + +
317A ALA* 2.9 24.9 + - - +
331A LEU* 3.8 26.2 - - + -
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Residues in contact with GLU 314 (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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310A LYS* 3.0 36.3 + - + +
311A THR* 3.3 28.4 + - - +
313A LEU* 1.3 76.6 - - + +
315A ALA* 1.3 58.1 + - - +
317A ALA* 2.9 3.3 + - - -
318A LYS* 2.8 61.0 + - - +
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A HIS* 5.4 3.8 - - + -
297A ILE* 3.7 27.6 - - + -
311A THR 2.9 17.2 + - - +
312A LEU 3.6 5.4 - - - +
314A GLU* 1.3 76.8 - - - +
316A VAL* 1.3 57.4 + - - +
318A LYS* 4.5 2.5 - - - +
319A LEU* 2.8 46.5 + - + +
324A THR* 4.2 1.8 - - - -
327A PHE* 4.1 13.0 - - + -
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Residues in contact with VAL 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A LEU 2.9 22.0 + - - +
313A LEU* 3.6 5.8 - - + +
315A ALA* 1.3 76.5 - - - +
317A ALA* 1.3 60.5 + - - +
319A LEU 3.5 13.3 - - - +
321A THR* 6.0 0.5 - - - -
324A THR* 3.8 16.9 + - - +
327A PHE* 3.9 20.6 - - + -
328A ARG* 3.5 26.7 - - + -
331A LEU* 3.6 21.8 - - + -
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Residues in contact with ALA 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LEU 2.9 16.0 + - - +
314A GLU* 3.5 4.9 - - - +
316A VAL* 1.3 79.8 - - - +
318A LYS* 1.3 71.5 + - + +
319A LEU 4.7 1.0 - - - +
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Residues in contact with LYS 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLU* 2.8 56.4 + - + +
315A ALA* 4.3 2.5 - - - +
317A ALA* 1.3 90.2 - - + +
319A LEU* 1.3 71.3 + - + +
320A PRO* 4.5 1.6 - - - +
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ILE* 5.6 0.2 - - + -
315A ALA* 2.8 37.9 + - + +
316A VAL 3.5 15.2 - - - +
317A ALA 4.7 0.7 - - - +
318A LYS* 1.3 83.7 - - + +
320A PRO* 1.3 78.5 - - + +
321A THR 3.6 1.2 + - - -
323A LYS* 4.9 7.9 - - + -
324A THR* 3.9 13.0 - - + +
411A TYR* 3.3 42.0 - - + +
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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