Contacts of the helix formed by residues 315 - 328 (chain A) in PDB entry 4FO9
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 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A ILE 3.7 3.2 + - - -
314A ARG* 1.3 76.4 - - + +
316A PRO* 1.3 77.9 - - - +
317A ASP* 2.9 38.8 + - - +
318A HIS* 3.0 27.2 + - + +
319A SER 4.0 1.4 + - - -
400A ASP* 5.0 1.7 - - - +
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Residues in contact with PRO 316 (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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313A ILE* 6.2 0.7 - - + -
314A ARG 3.3 5.4 - - - +
315A ASN* 1.3 90.4 - - - +
317A ASP* 1.3 59.5 + - - +
318A HIS 3.5 0.2 + - - -
319A SER 3.5 2.8 + - - -
320A ARG* 3.3 37.9 + - - +
400A ASP* 4.9 0.4 - - - +
401A GLY* 3.9 13.9 - - - +
402A LEU* 3.7 27.2 - - + +
405A GLU* 3.0 29.6 - - + +
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Residues in contact with ASP 317 (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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315A ASN* 2.9 23.7 + - - +
316A PRO* 1.3 74.1 - - - +
318A HIS* 1.3 64.0 + - - +
320A ARG* 2.8 35.7 + - - +
321A ALA* 3.0 23.4 + - - +
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Residues in contact with HIS 318 (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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314A ARG* 3.3 42.3 + - + +
315A ASN* 3.0 18.4 + - + +
317A ASP* 1.3 78.3 - - - +
319A SER* 1.3 59.6 + - - +
321A ALA* 3.4 7.0 + - - +
322A LEU* 3.2 19.2 + - - +
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Residues in contact with SER 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ARG* 5.3 1.7 - - - +
315A ASN 4.0 1.4 + - - -
316A PRO 3.5 4.5 + - - -
317A ASP 3.3 0.4 - - - -
318A HIS* 1.3 76.0 - - - +
320A ARG* 1.3 60.1 + - - +
322A LEU* 3.3 8.0 + - - +
323A ILE* 2.9 28.4 + - - +
358A ARG* 4.4 7.9 - - - +
365A LEU* 4.5 12.9 - - - +
400A ASP* 3.5 33.7 - - - -
402A LEU* 4.1 18.5 - - - +
403A PHE* 5.3 0.2 - - - -
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Residues in contact with ARG 320 (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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316A PRO* 3.3 24.8 + - - +
317A ASP* 2.8 43.9 + - - +
319A SER* 1.3 77.6 - - - +
321A ALA* 1.3 56.8 + - - +
323A ILE* 3.3 9.1 + - - +
324A LYS* 3.0 28.6 + - - +
402A LEU* 3.8 28.5 - - + +
405A GLU* 3.5 24.9 + - - -
422A GLY* 4.5 28.6 + - - +
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Residues in contact with ALA 321 (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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317A ASP 3.0 11.8 + - - +
318A HIS* 3.7 10.5 - - - +
319A SER 3.3 0.2 - - - -
320A ARG* 1.3 74.0 - - - +
322A LEU* 1.3 60.3 + - - +
324A LYS* 4.5 4.3 - - - +
325A GLU* 2.8 35.7 + - + +
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Residues in contact with LEU 322 (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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318A HIS 3.2 12.9 + - - +
319A SER* 3.3 9.8 + - - +
321A ALA* 1.3 74.0 - - - +
323A ILE* 1.3 67.4 + - - +
325A GLU* 3.7 4.0 - - - +
326A LYS* 2.9 31.4 + - + +
363A THR* 5.2 10.5 - - - +
365A LEU* 4.0 21.8 - - + -
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Residues in contact with ILE 323 (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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319A SER 2.9 15.1 + - - +
320A ARG* 3.3 12.5 + - - +
322A LEU* 1.3 77.9 - - - +
324A LYS* 1.3 57.4 + - - +
326A LYS* 3.5 1.4 - - - +
327A LEU* 3.0 35.9 + - + +
340A LEU* 4.1 19.6 - - + +
365A LEU* 4.7 10.2 - - + +
402A LEU* 6.2 1.1 - - + -
418A PHE* 5.2 15.7 - - + -
419A GLN 5.3 3.8 - - - +
420A GLU 5.5 0.9 - - - +
422A GLY* 5.2 8.5 - - - -
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Residues in contact with LYS 324 (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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320A ARG 3.0 15.4 + - - +
321A ALA* 4.3 4.3 - - - +
323A ILE* 1.3 71.8 - - - +
325A GLU* 1.3 57.5 + - - +
326A LYS 3.1 4.5 - - - -
327A LEU* 3.9 4.7 - - - +
328A THR* 3.0 31.7 + - - -
420A GLU* 4.1 20.2 + - - +
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Residues in contact with GLU 325 (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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321A ALA* 2.8 25.7 + - + +
322A LEU* 3.7 4.0 - - - +
324A LYS* 1.3 71.6 - - - +
326A LYS* 1.3 57.4 + - - +
328A THR* 4.4 9.9 - - - +
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Residues in contact with LYS 326 (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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322A LEU* 2.9 22.8 + - + +
323A ILE* 3.5 5.4 - - - +
324A LYS 3.1 0.2 - - - -
325A GLU* 1.3 79.1 - - - +
327A LEU* 1.3 62.2 - - + +
328A THR 3.2 11.1 + - - +
340A LEU* 4.6 11.0 - - + -
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Residues in contact with LEU 327 (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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323A ILE* 3.0 21.4 + - + +
324A LYS* 3.9 4.3 - - - +
326A LYS* 1.3 75.1 - - + +
328A THR* 1.3 61.6 + - - +
338A THR* 4.1 29.2 + - - +
339A SER* 4.3 12.6 - - - +
340A LEU* 4.1 33.4 - - + +
418A PHE* 4.3 5.8 - - + +
419A GLN* 3.9 29.6 - - - +
420A GLU* 4.4 8.3 - - + +
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Residues in contact with THR 328 (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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324A LYS 3.0 19.8 + - - -
325A GLU* 4.5 9.2 - - - +
326A LYS 3.2 8.3 - - - +
327A LEU* 1.3 81.5 - - - +
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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