Contacts of the helix formed by residues 324 - 334 (chain A) in PDB entry 5K9S
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 THR 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A ASN* 3.2 22.4 - - + +
323A GLY* 1.3 74.3 - - - -
325A ASP* 1.3 61.6 + - - +
326A GLU* 3.3 16.9 + - - +
327A GLN* 2.7 40.0 + - - +
328A THR* 2.9 31.4 + - - -
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Residues in contact with ASP 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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324A THR* 1.3 73.0 - - - +
326A GLU* 1.3 65.4 + - - +
328A THR* 4.4 3.4 - - - -
329A GLN* 3.0 12.3 + - - +
364A ALA 5.0 0.2 - - - +
365A GLY* 3.8 19.6 - - - -
366A ARG* 3.5 44.8 + - + +
369A GLN* 3.0 27.0 + - - +
11C LYS* 4.0 11.4 - - - -
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Residues in contact with GLU 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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324A THR* 3.1 12.9 + - - +
325A ASP* 1.3 87.6 + - - +
327A GLN* 1.3 65.9 + - + +
329A GLN* 3.4 7.9 + - - +
330A LYS* 3.3 27.2 + - - +
366A ARG* 3.6 16.6 + - - +
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Residues in contact with GLN 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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283A ASN* 3.5 22.0 + - - +
286A ILE* 3.5 23.9 - - + +
287A GLU* 3.0 30.7 + - - +
290A VAL* 4.6 9.6 - - + -
320A ILE* 3.9 30.1 - - + +
323A GLY* 3.3 8.5 - - - -
324A THR* 2.7 47.2 + - - +
326A GLU* 1.3 74.2 - - + +
328A THR* 1.3 67.0 + - - +
330A LYS* 3.2 19.4 + - + +
331A VAL 3.5 6.8 + - - -
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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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320A ILE 4.5 0.4 + - - -
321A VAL* 3.6 34.1 + - + +
324A THR 2.9 12.5 + - - -
325A ASP* 3.8 5.6 - - - -
327A GLN* 1.3 75.4 - - - +
329A GLN* 1.3 64.1 + - - +
331A VAL* 2.9 14.7 + - - +
332A ILE* 3.1 18.5 + - + +
362A ILE* 4.1 19.7 - - + -
369A GLN* 4.1 13.2 - - - +
11C LYS* 2.6 33.5 + - - +
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Residues in contact with GLN 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 ASP 3.0 18.5 + - - +
326A GLU* 3.6 8.5 - - - +
327A GLN 3.2 0.6 - - - -
328A THR* 1.3 76.2 - - - +
330A LYS* 1.3 57.5 + - + +
332A ILE* 3.2 9.4 + - - +
333A ASP* 2.7 64.4 + - - +
366A ARG* 3.1 19.1 + - - +
368A ASP* 3.7 3.3 - - - +
369A GLN* 2.9 35.1 + - - +
372A GLN* 3.1 23.6 + - - +
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Residues in contact with LYS 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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287A GLU* 4.3 8.5 + - - -
290A VAL* 3.3 40.3 + - + +
291A LYS* 5.0 3.6 - - - +
295A VAL* 3.7 17.5 - - + +
326A GLU* 3.3 15.9 + - - +
327A GLN* 3.2 10.2 + - - +
328A THR 3.1 0.8 - - - -
329A GLN* 1.3 78.3 - - + +
331A VAL* 1.3 62.7 + - - +
333A ASP* 3.8 11.5 - - - +
334A ALA* 3.1 23.9 + - - +
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Residues in contact with VAL 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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295A VAL* 3.9 16.8 - - + -
299A VAL* 4.3 0.2 - - - +
317A ILE* 3.7 27.8 - - + -
320A ILE* 3.7 32.3 - - + -
321A VAL* 3.8 20.0 - - + -
327A GLN 3.9 2.0 - - - +
328A THR 2.9 9.0 + - - +
330A LYS* 1.3 77.6 - - - +
332A ILE* 1.3 64.7 + - + +
334A ALA* 3.4 8.8 + - - +
335A GLY 3.6 0.3 + - - -
336A ALA* 3.3 38.3 + - + +
340A PHE* 5.8 0.2 - - + -
362A ILE* 5.2 6.1 - - + -
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Residues in contact with ILE 332 (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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328A THR* 3.1 14.6 + - + +
329A GLN* 3.2 9.4 + - - +
331A VAL* 1.3 78.0 - - + +
333A ASP* 1.3 63.6 + - - +
335A GLY* 3.0 15.6 + - - -
336A ALA 4.1 2.9 + - - +
337A LEU* 3.8 33.7 + - + +
362A ILE* 4.3 21.1 - - + -
369A GLN* 4.0 44.2 - - + +
372A GLN* 3.4 36.1 - - - +
376A HIS* 5.4 4.0 + - + -
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Residues in contact with ASP 333 (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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329A GLN* 2.7 56.3 + - - +
330A LYS* 3.8 11.9 - - - +
332A ILE* 1.3 73.5 - - - +
334A ALA* 1.3 59.1 + - - +
335A GLY* 3.1 1.8 + - - -
372A GLN* 5.6 0.7 + - - -
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Residues in contact with ALA 334 (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 VAL* 4.0 5.4 - - + -
296A PRO* 3.9 29.2 - - + +
299A VAL* 3.4 36.9 - - + +
330A LYS 3.1 17.3 + - - +
331A VAL 3.7 1.1 - - - +
332A ILE 3.2 0.6 - - - -
333A ASP* 1.3 75.8 - - - +
335A GLY* 1.3 57.3 + - - +
336A ALA 3.6 0.7 - - - -
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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