Contacts of the helix formed by residues 325 - 335 (chain A) in PDB entry 1WK8
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 GLY 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A ALA 3.7 0.8 + - - -
322A PRO 3.8 4.3 + - - +
323A ALA 3.8 1.6 - - - -
324A PHE* 1.3 81.3 - - - +
326A ALA* 1.3 60.4 + - - -
327A GLU* 3.3 2.7 - - - -
328A ASP* 3.3 17.1 + - - +
329A LEU* 2.9 28.1 + - - +
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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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325A GLY* 1.3 69.2 - - - -
327A GLU* 1.3 63.3 + - + +
329A LEU* 3.3 9.2 + - - +
330A GLU* 2.9 39.7 + - - +
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Residues in contact with GLU 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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308A TYR* 3.5 57.4 - - + +
325A GLY 3.3 0.2 - - - -
326A ALA* 1.3 76.2 - - + +
328A ASP* 1.3 66.5 + - - +
330A GLU* 3.2 13.6 + - - +
331A THR* 2.9 33.6 + - - -
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Residues in contact with ASP 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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238A VAL* 5.9 0.3 - - - +
308A TYR* 5.2 1.6 - - - -
318A VAL* 5.7 0.6 - - - +
319A HIS 3.7 6.6 - - - +
320A GLN* 3.4 32.7 + - - +
321A ALA* 2.9 47.9 + - - +
322A PRO* 4.3 2.9 - - + +
324A PHE* 4.5 4.2 - - - +
325A GLY* 3.4 18.6 - - - +
326A ALA 3.2 0.2 - - - -
327A GLU* 1.3 83.4 - - - +
329A LEU* 1.3 57.1 + - - +
331A THR* 3.3 2.6 + - - -
332A ALA* 2.8 30.0 + - - +
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Residues in contact with LEU 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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322A PRO* 4.0 27.3 - - + +
325A GLY 2.9 13.6 + - - +
326A ALA* 3.3 11.2 + - - +
328A ASP* 1.3 77.4 - - - +
330A GLU* 1.3 63.3 + - + +
332A ALA* 3.3 2.9 + - - +
333A ARG* 3.0 31.4 + - + +
339A LEU* 4.2 32.0 - - + +
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Residues in contact with GLU 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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326A ALA* 2.9 25.6 + - - +
327A GLU* 3.2 11.9 + - - +
329A LEU* 1.3 78.9 - - + +
331A THR* 1.3 61.0 + - - +
333A ARG* 3.3 16.7 + - - +
334A VAL* 2.9 34.1 + - + +
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Residues in contact with THR 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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239A ALA* 5.8 1.1 - - + -
304A VAL* 3.8 30.3 - - + -
305A LEU 4.5 7.1 + - - +
306A ALA* 4.3 3.0 - - + +
308A TYR* 2.7 37.1 + - - +
320A GLN* 4.1 7.6 - - + +
327A GLU 2.9 9.6 + - - -
328A ASP 3.7 3.8 - - - +
330A GLU* 1.3 75.6 - - - +
332A ALA* 1.3 64.6 + - - +
334A VAL* 3.2 7.3 + - - +
335A TYR* 3.2 35.8 + - + -
337A LEU* 5.1 0.6 - - + +
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Residues in contact with ALA 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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238A VAL* 4.7 4.7 - - + -
322A PRO* 3.7 24.0 - - + -
328A ASP 2.8 17.2 + - - +
329A LEU 3.3 5.6 + - - +
331A THR* 1.3 78.0 - - - +
333A ARG* 1.3 56.9 + - - +
335A TYR 3.1 2.4 + - - -
336A GLY 2.9 9.4 + - - -
337A LEU* 2.8 51.9 + - + +
339A LEU* 4.1 9.9 - - + -
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Residues in contact with ARG 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 LEU* 3.0 19.6 + - + +
330A GLU* 3.4 17.0 + - - +
332A ALA* 1.3 72.5 - - - +
334A VAL* 1.3 92.8 + - - +
336A GLY* 3.0 14.1 + - - +
337A LEU 4.8 2.0 + - - -
339A LEU* 5.0 4.2 - - + +
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Residues in contact with VAL 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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330A GLU* 2.9 21.1 + - + +
331A THR* 3.2 11.2 + - - +
333A ARG* 1.3 102.6 - - - +
335A TYR* 1.3 79.0 + - + +
336A GLY 3.7 0.3 + - - -
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Residues in contact with TYR 335 (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 GLU* 2.5 34.9 + - + -
299A LYS* 2.7 34.9 + - - +
302A PHE* 3.7 22.4 - + + -
304A VAL* 3.6 29.8 - - + -
305A LEU* 3.1 31.5 + - - +
331A THR* 3.2 19.3 + - + +
332A ALA 3.1 1.6 + - - -
333A ARG 3.1 0.6 - - - -
334A VAL* 1.3 94.3 - - + +
336A GLY* 1.3 59.8 + - - +
337A LEU* 3.2 22.0 + - + +
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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