Contacts of the helix formed by residues 321 - 331 (chain A) in PDB entry 5I4A
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 321 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A GLU 3.1 27.8 - - - -
315A LEU* 2.4 26.6 + - - -
318A ASN* 3.0 14.7 + - - +
319A LYS 3.7 0.8 - - - -
320A HIS* 1.3 80.9 - - - +
322A VAL* 1.3 60.4 + - - +
323A PHE 3.3 8.4 + - - -
324A TYR* 3.2 11.3 + - - -
325A ARG* 2.9 29.7 + - - +
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Residues in contact with VAL 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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315A LEU* 3.8 21.1 - - + -
321A SER* 1.3 72.7 - - - +
323A PHE* 1.3 60.4 + - - +
325A ARG* 3.5 28.0 - - + +
326A ALA* 2.9 29.3 + - - +
407A ILE* 4.5 11.0 - - + -
409A PRO* 4.1 30.3 - - + +
412A ILE* 4.1 11.9 - - + -
413A LYS* 4.3 17.5 - - + -
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Residues in contact with PHE 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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293A LEU* 4.2 21.3 - - + -
315A LEU* 3.9 13.5 - - + +
316A PHE* 3.7 35.7 - + + -
321A SER* 3.1 10.2 + - - +
322A VAL* 1.3 83.6 - - - +
324A TYR* 1.3 73.3 + + - +
326A ALA* 3.7 3.3 - - - +
327A ALA* 3.1 20.1 + - - +
335A VAL* 3.9 25.4 - - + -
337A PHE* 3.9 10.3 - + - -
373A ILE* 5.0 2.2 - - + -
412A ILE* 3.8 18.8 - - + -
415A TYR* 4.8 8.3 - + - -
416A VAL* 3.6 23.9 - - + +
419A MET* 4.6 19.1 - - + -
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Residues in contact with TYR 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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315A LEU 3.3 13.7 - - - -
316A PHE* 2.8 25.3 + - - -
318A ASN 3.1 27.4 - - - -
319A LYS* 3.3 47.3 - - + +
320A HIS* 4.4 0.9 - - - -
321A SER* 3.2 16.3 + - - +
323A PHE* 1.3 79.2 - + - +
325A ARG* 1.3 61.2 + - - +
327A ALA* 3.4 4.5 + - - +
328A ALA* 3.0 28.9 + - - +
335A VAL* 3.8 39.2 - - + +
337A PHE* 3.1 24.4 - + - -
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Residues in contact with ARG 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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318A ASN* 5.6 0.2 - - - +
320A HIS* 2.7 41.1 + - + +
321A SER* 2.9 27.6 + - - +
322A VAL* 3.5 27.9 - - + +
324A TYR* 1.3 73.6 - - - +
326A ALA* 1.3 56.4 + - - +
328A ALA* 3.7 5.4 - - - +
329A GLU* 2.7 54.2 + - - +
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Residues in contact with ALA 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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282A PHE* 4.2 15.7 - - + -
322A VAL 2.9 19.1 + - - +
323A PHE* 3.7 5.2 - - - +
325A ARG* 1.3 77.5 - - - +
327A ALA* 1.3 57.0 + - - +
329A GLU* 3.3 11.1 + - - +
330A LEU* 2.9 36.6 + - - +
413A LYS* 4.2 15.9 - - + -
416A VAL* 4.1 20.6 - - + -
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Residues in contact with ALA 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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293A LEU* 4.2 5.2 - - + -
323A PHE* 3.1 16.0 + - + +
324A TYR 3.4 2.9 + - - +
325A ARG 3.3 0.2 - - - -
326A ALA* 1.3 76.3 - - - +
328A ALA* 1.3 60.3 + - - +
330A LEU 3.4 0.3 + - - -
331A GLY 3.2 4.3 + - - -
332A PHE* 3.0 51.0 + - + -
335A VAL* 3.6 30.7 - - + -
416A VAL* 3.9 10.0 - - + +
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Residues in contact with ALA 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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285A SER* 4.7 0.3 + - - -
324A TYR 3.0 17.4 + - - +
325A ARG* 3.7 6.7 - - - +
327A ALA* 1.3 74.7 - - - +
329A GLU* 1.3 64.9 + - + +
331A GLY* 3.0 14.2 + - - -
332A PHE 4.7 8.0 - - - +
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Residues in contact with GLU 329 (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 VAL 4.0 1.6 - - - +
282A PHE* 3.5 47.4 - - + +
283A LYS 5.5 0.3 - - - -
285A SER* 3.1 28.8 + - - -
325A ARG* 2.7 42.6 + - - +
326A ALA* 3.7 6.5 - - - +
328A ALA* 1.3 72.6 - - + +
330A LEU* 1.3 59.8 + - - +
413A LYS* 4.6 6.9 + - - -
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Residues in contact with LEU 330 (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 VAL* 3.9 24.7 - - + +
282A PHE* 3.6 33.9 - - + -
285A SER* 3.1 6.7 - - - -
286A PHE* 3.0 57.5 + - + +
289A ASN* 3.2 4.7 + - - -
326A ALA 2.9 19.9 + - - +
327A ALA 4.0 3.6 - - - +
328A ALA 3.2 0.2 - - - -
329A GLU* 1.3 72.4 - - - +
331A GLY* 1.3 58.5 + - - +
332A PHE* 3.7 9.6 - - + -
416A VAL* 4.0 13.2 - - + +
417A TYR* 3.7 33.7 - - + +
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Residues in contact with GLY 331 (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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271A LYS* 6.2 0.4 - - - -
285A SER* 3.2 13.2 + - - -
289A ASN* 3.4 9.4 - - - -
290A GLU* 3.1 26.0 + - - +
328A ALA 3.0 14.3 + - - -
330A LEU* 1.3 76.5 - - - +
332A PHE* 1.3 65.4 + - - +
333A SER* 3.5 0.5 + - - -
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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