Contacts of the helix formed by residues 323 - 339 (chain A) in PDB entry 2DW1
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 ILE 323 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ARG* 4.4 0.7 - - - -
321A SER* 2.8 18.6 + - - +
322A GLU* 1.3 77.9 - - + +
324A ASN* 1.3 64.9 - - - +
325A LEU* 3.8 17.9 - - + +
326A VAL* 2.9 36.6 + - + +
327A VAL* 3.3 4.7 + - - +
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Residues in contact with ASN 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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224A ARG* 2.8 45.4 + - - +
227A GLU* 4.1 28.8 + - + +
228A ILE* 3.9 15.0 - - + +
231A THR* 5.1 3.5 + - - +
322A GLU 3.3 5.1 + - - +
323A ILE* 1.3 71.6 - - - +
325A LEU* 1.3 57.9 + - - +
327A VAL* 4.1 1.5 - - - +
328A ALA* 2.9 31.7 + - - +
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Residues in contact with LEU 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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231A THR* 4.3 15.7 - - + -
235A ILE* 5.3 0.2 - - + -
323A ILE* 3.1 13.8 + - + +
324A ASN* 1.3 77.3 - - - +
326A VAL* 1.3 59.0 + - + +
328A ALA* 3.4 5.4 + - - +
329A VAL* 2.9 42.1 + - + +
365A PRO* 4.0 25.8 - - + +
367A THR* 3.7 29.8 - - + -
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Residues in contact with VAL 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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320A TYR* 3.7 32.1 - - + -
321A SER* 3.8 14.4 - - - +
323A ILE* 2.9 39.7 + - + +
325A LEU* 1.3 77.0 - - + +
327A VAL* 1.3 65.6 + - - +
329A VAL* 3.1 17.1 + - - +
330A ILE* 3.1 17.9 + - + +
361A ILE* 3.7 16.4 - - + -
365A PRO* 4.6 15.5 - - + -
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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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224A ARG* 3.4 12.3 - - - +
228A ILE* 3.5 31.4 - - + -
290A LEU* 4.5 12.3 - - + -
317A ILE* 4.4 17.7 - - + -
318A GLN 4.9 1.6 - - - +
319A ASP* 4.2 9.9 - - - +
320A TYR* 4.7 5.4 - - + +
321A SER 3.2 34.5 - - - +
323A ILE 3.3 2.9 + - - +
324A ASN 4.2 2.2 - - - +
326A VAL* 1.3 75.7 - - + +
328A ALA* 1.3 63.1 + - - +
330A ILE* 3.2 8.9 + - + +
331A MET* 3.0 25.5 + - + +
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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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228A ILE* 3.6 19.7 - - + +
231A THR* 3.7 35.7 - - + -
232A VAL* 3.7 9.1 - - + +
235A ILE* 4.1 3.6 - - + +
324A ASN 2.9 21.5 + - - +
325A LEU 3.5 5.8 - - - +
326A VAL 3.2 0.2 - - - -
327A VAL* 1.3 78.0 - - - +
329A VAL* 1.3 56.1 + - - +
331A MET 3.7 0.2 + - - -
332A ALA* 3.1 27.7 + - - +
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Residues in contact with VAL 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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2A GM6 5.3 2.5 - - + -
235A ILE* 4.8 6.7 - - + -
325A LEU* 2.9 27.3 + - + +
326A VAL* 3.1 9.8 + - - +
328A ALA* 1.3 76.7 - - - +
330A ILE* 1.3 68.3 + - + +
332A ALA* 3.3 5.8 + - - +
333A HIS* 2.9 21.6 + - + +
356A ILE* 4.2 24.6 - - + +
361A ILE* 4.5 19.1 - - + -
365A PRO* 3.8 18.6 - - + -
366A SER 3.8 21.5 - - - +
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Residues in contact with ILE 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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2A GM6 3.5 21.1 - - + -
299A ILE* 3.4 49.8 - - + +
300A GLY* 4.3 1.6 - - - -
317A ILE* 3.8 18.2 - - + -
318A GLN 5.0 5.2 - - - +
320A TYR* 4.7 4.0 - - + -
326A VAL* 3.1 16.4 - - + +
327A VAL* 3.6 12.1 - - - +
329A VAL* 1.3 75.1 - - - +
331A MET* 1.3 60.1 - - - +
333A HIS* 3.0 8.9 + - - +
334A GLU* 2.8 43.6 + - + +
361A ILE* 3.5 18.6 - - + -
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Residues in contact with MET 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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202A LEU* 4.1 23.6 - - - -
204A LEU* 3.7 30.1 - - + -
225A MET* 4.9 0.2 - - + -
228A ILE* 3.8 20.2 - - + -
229A VAL* 4.5 6.1 - - - -
232A VAL* 3.8 22.0 - - + -
288A GLN* 4.6 2.9 - - + -
290A LEU* 4.2 13.0 - - + -
317A ILE* 3.5 29.8 - - + +
327A VAL* 3.0 16.3 + - + +
328A ALA* 3.8 4.3 - - - +
330A ILE* 1.3 76.8 - - - +
332A ALA* 1.3 61.7 + - - +
334A GLU* 3.2 2.3 + - - +
335A MET* 2.9 37.4 + - + +
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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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232A VAL* 4.3 6.2 - - + +
235A ILE* 3.9 25.6 - - + -
236A TYR* 2.8 45.0 + - + -
328A ALA 3.1 18.9 + - - +
329A VAL 3.3 4.5 + - - +
331A MET* 1.3 76.5 - - - +
333A HIS* 1.3 57.0 + - - +
335A MET* 4.6 1.1 - - - -
336A GLY* 2.8 11.6 + - - -
356A ILE* 4.4 10.3 - - + -
369A PHE* 3.9 3.9 - - + -
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Residues in contact with HIS 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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2A GM6 3.5 29.6 + - + +
329A VAL* 2.9 13.8 + - + +
330A ILE* 3.1 15.5 - - - +
332A ALA* 1.3 76.2 - - - +
334A GLU* 1.3 67.8 + - - +
336A GLY* 3.0 10.4 + - - -
337A HIS* 3.1 12.5 + - - -
343A HIS* 3.3 6.3 + + - -
356A ILE* 2.6 25.8 + - + +
357A MET* 3.5 27.9 - - + +
358A ARG 3.2 25.8 - - - -
700A ZN 2.3 36.0 - - - -
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Residues in contact with GLU 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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2A GM6 2.6 41.2 + - - +
288A GLN* 3.8 19.7 - - - +
300A GLY* 3.2 12.3 - - - -
301A LEU 3.4 9.9 - - - +
302A ALA* 3.4 32.3 + - + +
316A ILE 4.1 6.1 - - - +
317A ILE* 4.0 18.8 - - + -
330A ILE* 2.8 24.8 + - + +
331A MET 3.2 2.4 + - - +
333A HIS* 1.3 76.7 - - - +
335A MET* 1.3 65.8 + - - +
337A HIS* 3.4 2.5 + - - -
338A ASN* 3.2 20.0 + - - -
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Residues in contact with MET 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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200A VAL* 3.5 39.7 - - + -
202A LEU* 4.2 24.9 - - - -
232A VAL* 4.4 12.8 - - - -
236A TYR* 3.5 15.7 - - + +
241A ILE* 6.2 0.2 - - + -
243A VAL* 4.1 16.8 - - + -
286A ASN* 4.0 5.8 - - - +
288A GLN* 3.7 20.9 - - + +
307A MET* 4.3 6.1 - - + -
331A MET* 2.9 28.0 + - + +
332A ALA 4.0 0.7 - - - +
334A GLU* 1.3 74.0 - - - +
336A GLY* 1.3 65.7 + - - +
338A ASN* 3.1 11.3 + - + +
339A LEU* 2.8 28.3 + - + +
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Residues in contact with GLY 336 (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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236A TYR* 3.1 13.0 + - - -
332A ALA 2.8 13.2 + - - -
333A HIS 3.0 6.1 + - - -
335A MET* 1.3 76.7 - - - +
337A HIS* 1.3 62.5 + - - +
339A LEU* 2.9 13.9 + - - -
341A ILE* 3.0 39.0 + - - +
357A MET* 4.3 5.6 - - - -
369A PHE* 4.9 0.4 - - - -
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Residues in contact with HIS 337 (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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2A GM6 3.1 12.1 - - - -
302A ALA* 4.0 12.8 - - + +
303A TYR 3.2 15.5 - - - +
304A VAL* 3.0 15.1 - - + +
305A GLY 2.7 30.5 + - - -
333A HIS* 3.1 15.9 + - - -
334A GLU* 3.6 15.3 - - - +
336A GLY* 1.3 73.3 - - - +
338A ASN* 1.3 51.8 + - - +
340A GLY* 2.8 8.8 + - - -
341A ILE 2.8 27.7 + - - -
342A ASN* 4.3 2.5 - - - -
343A HIS* 2.9 27.5 + + - -
357A MET* 3.7 6.9 - - + +
700A ZN 2.1 37.2 - - - -
565B PRO* 6.2 0.7 - - + -
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Residues in contact with ASN 338 (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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286A ASN* 2.9 31.4 + - - +
288A GLN* 3.0 19.2 - - - +
302A ALA* 3.6 2.2 - - - +
303A TYR 3.0 18.8 + - - +
305A GLY* 3.4 0.3 - - - -
306A SER* 2.9 37.3 + - - +
307A MET* 3.1 18.4 + - + +
314A THR 3.0 28.1 + - - +
334A GLU 3.2 10.6 + - - +
335A MET* 3.1 10.8 + - - +
337A HIS* 1.3 76.9 - - - +
339A LEU* 1.3 56.5 + - - +
340A GLY 3.1 2.3 + - - -
380A PHE* 4.2 0.5 - - - -
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Residues in contact with LEU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A VAL* 4.8 4.7 - - + -
236A TYR* 3.5 35.9 - - + +
241A ILE* 3.7 27.6 - - + -
307A MET* 3.6 33.4 - - + -
335A MET* 2.8 20.5 + - + +
336A GLY* 2.9 8.0 + - - +
338A ASN* 1.3 74.5 - - - +
340A GLY* 1.3 58.7 + - - +
341A ILE* 3.3 4.2 + - + -
377A CYS* 3.8 23.7 - - - +
380A PHE* 3.6 24.6 - - + +
381A ILE* 5.2 4.5 - - + -
386A PRO* 6.0 0.4 - - + -
389A ILE* 4.6 13.2 - - + -
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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