Contacts of the helix formed by residues 384 - 403 (chain A) in PDB entry 2W2M
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 384 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A ASN* 4.0 9.2 - - - -
338A ALA* 3.8 6.7 - - - +
346A VAL* 5.7 0.2 - - - -
348A LEU* 4.3 9.1 - - - +
365A GLY* 2.8 19.3 + - - +
383A SER* 1.3 74.5 - - - +
385A THR* 1.3 63.9 + - - -
386A SER 3.2 2.7 - - - -
387A GLN* 3.3 6.3 + - - +
388A ALA 3.3 15.9 + - - -
152P GLN 3.5 11.4 - - - -
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Residues in contact with THR 385 (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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314A ALA* 3.4 12.2 - - - +
315A ALA* 3.7 5.4 - - + -
316A GLY* 3.1 31.8 + - - +
317A ASN* 2.8 26.3 + - - +
336A VAL 3.6 15.2 - - - +
337A GLY* 4.0 1.1 - - - -
338A ALA* 3.7 14.1 - - + +
348A LEU* 6.1 0.4 - - + -
353A THR* 3.5 23.6 - - - +
384A GLY* 1.3 69.4 - - - -
386A SER* 1.3 59.5 + - - +
388A ALA* 3.5 7.1 - - - +
389A ALA* 2.9 30.0 + - - +
152P GLN* 3.3 3.0 + - - +
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Residues in contact with SER 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A HIS* 3.2 12.7 + - - -
230A LEU* 3.5 14.5 - - - +
286A LEU* 4.9 0.2 - - - +
288A PRO* 2.9 40.8 + - - +
314A ALA* 3.9 3.3 - - - +
385A THR* 1.3 76.8 + - - +
387A GLN* 1.3 63.3 + - - +
389A ALA* 3.3 3.5 + - - +
390A ALA* 3.0 23.6 + - - +
152P GLN* 2.8 32.9 + - - -
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Residues in contact with GLN 387 (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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226A HIS* 4.8 4.4 - - - -
229A HIS* 3.2 29.1 + - + +
230A LEU* 3.5 22.2 - - + +
233A VAL* 4.0 2.1 - - + +
364A PRO 3.8 0.4 - - - -
365A GLY* 4.3 2.5 - - - -
368A ILE* 4.0 22.0 - - + -
382A GLN* 3.1 43.9 + - - +
383A SER 3.2 23.3 - - - +
384A GLY* 3.3 9.5 + - - +
386A SER* 1.3 82.5 - - - +
388A ALA* 1.3 63.9 - - - +
390A ALA* 3.3 4.4 + - - +
391A HIS* 2.8 30.7 + - - -
152P GLN* 4.5 1.4 - - - +
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Residues in contact with ALA 388 (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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336A VAL* 3.8 7.4 - - + +
337A GLY 3.4 28.0 - - - +
338A ALA* 3.9 10.1 - - - -
363A ALA* 3.4 18.7 - - - +
364A PRO 3.3 13.9 + - - +
384A GLY 3.3 4.1 + - - +
385A THR* 3.5 13.2 - - - +
386A SER 3.3 0.2 - - - -
387A GLN* 1.3 77.8 - - - +
389A ALA* 1.3 61.0 + - - +
391A HIS* 3.1 21.0 + - - +
392A VAL 3.4 4.0 + - - -
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Residues in contact with ALA 389 (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 LEU* 3.7 17.7 - - + -
288A PRO* 5.4 0.4 - - + -
312A VAL* 3.3 11.7 - - + +
313A THR 3.6 28.3 - - - +
314A ALA* 3.9 1.8 - - - +
336A VAL* 3.8 12.7 - - + +
385A THR 2.9 18.5 + - - +
386A SER* 3.7 4.7 - - - +
388A ALA* 1.3 74.9 - - - +
390A ALA* 1.3 58.0 + - - +
392A VAL 3.2 1.0 + - - -
393A ALA* 2.9 26.9 + - - +
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Residues in contact with ALA 390 (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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230A LEU* 4.0 9.9 - - + +
233A VAL* 3.6 22.5 - - + +
234A VAL* 3.5 26.8 - - + +
286A LEU* 3.8 18.5 - - + +
386A SER 3.0 15.9 + - - +
387A GLN 3.6 7.2 - - - +
388A ALA 3.3 0.2 - - - -
389A ALA* 1.3 76.4 - - - +
391A HIS* 1.3 57.0 + - - +
393A ALA* 4.3 0.7 - - - -
394A GLY* 3.1 21.8 + - - -
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Residues in contact with HIS 391 (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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157A ASN* 2.9 38.6 + - + +
158A LEU* 4.8 0.2 - - + -
161A ILE* 4.2 20.9 - - + -
233A VAL* 3.7 14.5 - - + +
241A VAL* 3.7 26.0 - - + +
363A ALA* 4.1 10.5 - - + -
364A PRO* 3.2 27.9 + - + -
368A ILE* 3.8 14.4 - - + -
387A GLN 2.8 21.6 + - - -
388A ALA 3.1 10.4 + - - +
390A ALA* 1.3 78.8 - - - +
392A VAL* 1.3 57.7 + - - +
394A GLY* 3.3 2.4 + - - -
395A ILE* 2.9 33.6 + - + +
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Residues in contact with VAL 392 (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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312A VAL* 4.0 15.9 - - + -
334A ILE* 4.0 20.4 - - + -
336A VAL* 3.7 31.9 - - + -
361A LEU* 4.2 7.9 - - + -
363A ALA* 3.9 3.8 - - + -
388A ALA 3.4 0.4 + - - -
389A ALA 3.2 7.0 + - - +
391A HIS* 1.3 73.2 - - - +
393A ALA* 1.3 57.2 + - - +
395A ILE* 3.3 6.7 + - + +
396A ALA* 2.8 33.7 + - + +
415A LEU* 4.1 19.5 - - + +
442A ALA* 3.8 26.5 - - + -
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Residues in contact with ALA 393 (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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182A VAL* 4.7 4.4 - - + +
234A VAL* 4.5 7.2 - - + -
284A VAL* 4.1 21.1 - - + +
286A LEU* 4.1 24.9 - - + -
312A VAL* 4.0 13.0 - - + +
389A ALA 2.9 17.2 + - - +
390A ALA* 3.9 6.3 - - - +
392A VAL* 1.3 76.2 - - - +
394A GLY* 1.3 57.2 + - - +
396A ALA* 3.6 2.2 + - - +
397A ALA* 3.0 28.6 + - - +
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Residues in contact with GLY 394 (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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234A VAL* 4.4 10.5 - - - +
241A VAL* 3.6 19.1 - - - -
242A ALA* 3.5 13.8 - - - +
390A ALA 3.1 16.2 + - - -
391A HIS 3.3 4.0 + - - -
392A VAL 3.2 0.2 - - - -
393A ALA* 1.3 74.1 - - - +
395A ILE* 1.3 64.0 + - - +
397A ALA* 3.4 1.3 + - - -
398A MET* 3.0 25.6 + - - +
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Residues in contact with ILE 395 (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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161A ILE* 4.4 12.6 - - + -
241A VAL* 4.2 6.3 - - + -
391A HIS* 2.9 22.6 + - + +
392A VAL* 3.7 7.9 - - + +
394A GLY* 1.3 71.6 - - - +
396A ALA* 1.3 60.6 + - - +
398A MET* 3.0 5.0 + - - +
399A MET* 2.9 44.2 + - + +
415A LEU* 3.8 21.1 - - + -
442A ALA* 3.8 29.6 - - + -
443A ALA* 4.0 22.0 - - - +
444A LEU* 3.8 31.4 - - + +
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Residues in contact with ALA 396 (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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284A VAL* 4.4 11.4 - - + -
310A VAL* 4.5 7.0 - - + -
312A VAL* 5.1 2.2 - - + -
392A VAL 2.8 21.9 + - - +
393A ALA* 3.8 7.6 - - - +
395A ILE* 1.3 72.5 - - - +
397A ALA* 1.3 57.8 + - - +
399A MET* 3.4 4.5 + - - +
400A LEU* 3.0 36.7 + - + +
411A LEU* 4.0 31.2 - - + -
415A LEU* 4.9 6.2 - - + +
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Residues in contact with ALA 397 (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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176A GLY* 4.4 1.6 - - - -
177A GLY 4.4 9.0 - - - +
180A VAL* 3.8 16.3 - - + +
182A VAL* 4.0 23.1 - - + -
234A VAL* 5.7 0.2 - - + -
242A ALA* 4.4 10.3 - - + -
245A ALA* 5.0 1.8 - - + -
284A VAL* 4.3 2.4 - - + +
393A ALA 3.0 18.5 + - - +
394A GLY* 3.6 6.7 - - - +
395A ILE 3.2 0.2 - - - -
396A ALA* 1.3 73.0 - - - +
398A MET* 1.3 64.4 + - - +
400A LEU 3.5 1.0 + - - -
401A SER* 3.0 29.8 + - - -
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Residues in contact with MET 398 (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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176A GLY* 3.5 26.7 - - - -
241A VAL* 4.0 14.1 - - + +
242A ALA* 3.7 19.5 - - + -
243A LYS 5.1 0.7 - - - +
394A GLY 3.0 21.1 + - - +
395A ILE 3.0 7.5 + - - +
397A ALA* 1.3 75.5 - - - +
399A MET* 1.3 62.2 + - + +
401A SER* 3.3 4.3 + - - -
402A ALA* 3.3 21.0 + - - +
444A LEU* 3.7 34.1 - - + -
445A PRO* 6.0 0.7 - - + -
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Residues in contact with MET 399 (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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395A ILE* 2.9 34.3 + - + +
396A ALA 3.7 4.3 - - - +
398A MET* 1.3 77.5 - - + +
400A LEU* 1.3 57.6 + - - +
402A ALA* 3.4 7.6 + - - +
403A GLU* 2.9 30.4 + - - +
406A LEU* 3.9 11.1 - - + +
411A LEU* 4.0 24.0 - - + -
414A ARG* 3.8 40.2 - - + +
415A LEU* 4.1 13.7 - - + -
418A PHE* 4.2 7.2 - - + -
443A ALA 4.6 3.8 - - - +
445A PRO* 3.7 36.8 - - + -
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Residues in contact with LEU 400 (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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180A VAL* 3.6 20.0 - - + +
282A PRO* 3.9 25.2 - - + +
283A LEU 5.1 0.2 - - - +
284A VAL* 3.8 25.6 - - + -
310A VAL* 4.1 20.4 - - + -
396A ALA* 3.0 22.2 + - + +
399A MET* 1.3 74.2 - - - +
401A SER* 1.3 60.4 + - - +
403A GLU 3.8 14.8 - - - +
404A PRO* 3.2 32.4 - - - +
406A LEU* 4.1 26.0 - - + +
411A LEU* 4.1 14.4 - - + -
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Residues in contact with SER 401 (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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176A GLY* 3.3 11.8 - - - -
177A GLY 2.8 30.0 + - - -
178A SER* 3.5 16.6 + - - +
179A LEU* 5.7 1.1 - - - +
180A VAL* 3.5 9.0 - - - +
397A ALA 3.0 11.1 + - - -
398A MET 3.3 4.9 + - - -
400A LEU* 1.3 75.2 - - - +
402A ALA* 1.3 65.4 + - - +
404A PRO* 4.2 8.4 - - - +
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Residues in contact with ALA 402 (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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398A MET 3.3 10.1 + - - +
399A MET* 3.6 10.3 - - - +
401A SER* 1.3 81.2 - - - +
403A GLU* 1.3 69.4 + - + +
404A PRO* 3.6 5.6 - - - +
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Residues in contact with GLU 403 (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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399A MET 2.9 7.0 + - - +
400A LEU* 3.5 9.3 - - - +
402A ALA* 1.3 87.5 - - + +
404A PRO* 1.3 66.0 - - - +
405A GLU 3.2 4.1 + - - +
406A LEU* 3.3 39.1 + - + +
414A ARG* 2.9 37.5 + - - -
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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