Contacts of the helix formed by residues 320 - 331 (chain A) in PDB entry 5KYT
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 320 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A PRO* 4.1 1.4 - - - +
319A LEU* 1.3 79.6 - - - +
321A LYS* 1.3 63.1 + - - +
322A GLU* 3.8 12.0 + - - +
323A VAL* 2.9 38.2 + - - +
324A GLY* 3.0 17.5 + - - -
456A SER* 4.8 11.0 - - - -
459A LEU* 6.0 4.3 - - - -
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Residues in contact with LYS 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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319A LEU 3.4 3.7 + - - -
320A SER* 1.3 73.4 - - - +
322A GLU* 1.3 71.4 + - - +
324A GLY* 3.8 1.0 - - - +
325A GLU* 2.9 63.6 + - - +
359A PRO* 3.5 26.5 + - + +
360A GLY* 4.0 25.1 - - - +
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Residues in contact with GLU 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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320A SER* 3.8 7.2 - - - +
321A LYS* 1.3 96.7 + - - +
323A VAL* 1.3 63.1 + - + +
325A GLU* 3.8 8.1 - - - +
326A ALA* 2.9 30.3 + - - +
456A SER* 3.3 24.1 + - - +
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Residues in contact with VAL 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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292A PHE* 3.8 35.0 - - + +
293A SER* 5.7 0.7 - - - -
296A ALA* 4.5 8.3 - - + -
319A LEU* 4.5 4.9 - - + -
320A SER* 2.9 24.9 + - - +
322A GLU* 1.3 78.3 - - + +
324A GLY* 1.3 54.7 + - - +
326A ALA* 3.1 7.3 + - - +
327A VAL* 2.7 41.3 + - + +
459A LEU* 5.1 15.0 - - + -
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Residues in contact with GLY 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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292A PHE* 4.8 2.5 - - - -
319A LEU* 3.9 24.3 - - - +
320A SER 3.0 14.6 + - - -
321A LYS* 3.8 3.4 - - - -
323A VAL* 1.3 77.9 - - - +
325A GLU* 1.3 55.7 + - - +
327A VAL 3.9 0.2 - - - -
328A ALA* 2.9 31.6 + - - +
336A ILE* 3.4 13.9 - - - +
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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 LYS* 2.9 46.0 + - + +
322A GLU* 3.8 5.9 - - - +
324A GLY* 1.3 73.3 - - - +
326A ALA* 1.3 62.9 + - - +
328A ALA* 3.8 5.6 - - - +
329A LYS* 3.1 24.8 + - - +
335A GLY* 6.2 0.7 - - - -
359A PRO* 3.4 30.3 - - + +
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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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296A ALA* 5.4 10.5 - - + +
322A GLU 2.9 18.4 + - - +
323A VAL* 3.3 8.3 - - - +
325A GLU* 1.3 76.5 - - - +
327A VAL* 1.3 64.3 + - + +
329A LYS* 3.3 7.8 + - - +
330A ARG* 3.2 27.3 + - - +
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Residues in contact with VAL 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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287A LEU* 6.2 0.7 - - + -
292A PHE* 3.7 53.4 - - + +
295A PHE* 4.3 7.4 - - + +
296A ALA* 3.9 17.7 - - + +
312A ILE* 4.7 3.1 - - + -
323A VAL* 2.7 25.7 + - + +
324A GLY 4.0 1.8 - - - +
326A ALA* 1.3 68.4 - - - +
328A ALA* 1.3 68.3 + - - +
330A ARG* 3.3 8.3 + - - +
331A PHE* 3.0 47.8 + - + -
336A ILE* 4.7 4.0 - - + -
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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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324A GLY 2.9 18.2 + - - +
325A GLU* 3.8 6.3 - - - +
327A VAL* 1.3 78.8 - - - +
329A LYS* 1.3 60.5 + - - +
331A PHE* 3.2 3.6 + - - -
332A HIS 3.0 4.5 + - - -
333A LEU* 2.9 44.5 + - - +
334A PRO 4.5 0.7 - - - +
335A GLY* 3.6 31.2 - - - +
336A ILE* 3.8 8.7 - - + +
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Residues in contact with LYS 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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325A GLU 3.1 13.7 + - - +
326A ALA* 3.5 11.2 - - - +
327A VAL 3.2 0.2 - - - -
328A ALA* 1.3 76.3 - - - +
330A ARG* 1.3 63.9 + - + +
332A HIS* 3.0 21.2 + - - +
333A LEU 4.2 3.3 + - - -
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Residues in contact with ARG 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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295A PHE 3.4 15.7 - - - -
296A ALA* 3.2 28.7 - - - +
298A SER* 3.6 26.7 - - - +
301A ILE* 4.0 25.4 - - + +
326A ALA* 3.2 12.6 + - - +
327A VAL* 3.6 8.3 - - - +
329A LYS* 1.3 79.0 - - + +
331A PHE* 1.3 58.8 + - - +
332A HIS* 3.2 21.6 + - - -
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Residues in contact with PHE 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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273A PHE* 5.0 2.7 - + - -
274A LEU* 4.5 4.0 - - + -
277A LEU* 4.1 16.2 - - + -
287A LEU* 6.3 0.2 - - + -
295A PHE* 3.8 26.0 - + + -
301A ILE* 3.7 31.9 - - + -
306A LEU* 3.6 35.6 - - + +
309A LEU* 3.7 18.2 - - + +
312A ILE* 3.5 21.3 - - + -
327A VAL* 3.0 43.2 + - + +
328A ALA 4.0 0.7 - - - +
330A ARG* 1.3 73.5 - - - +
332A HIS* 1.3 72.5 + - - +
333A LEU* 3.3 25.5 + - + +
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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