Contacts of the helix formed by residues 329 - 348 (chain B) in PDB entry 6B0Z
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 PRO 329 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B ILE* 3.6 30.3 - - + -
26B ILE* 4.8 0.2 - - + -
327B THR 3.3 9.9 - - - +
328B ASN* 1.3 92.0 - - - +
330B ILE* 1.3 56.9 + - - +
331B ALA 3.4 2.0 - - - -
332B SER* 3.2 7.3 + - - +
333B ILE* 2.8 36.8 + - + +
373B THR* 4.3 0.4 - - + -
394B THR* 5.7 1.6 - - + +
397B PHE* 3.5 36.3 - - + -
398B MET* 3.7 26.7 - - + -
401B LEU* 4.4 0.2 - - + -
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Residues in contact with ILE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ILE* 3.6 24.9 - - + -
289B GLY 4.0 0.2 - - - +
290B MET* 3.6 27.4 - - + -
328B ASN* 3.0 20.9 + - - +
329B PRO* 1.3 77.2 - - - +
331B ALA* 1.3 57.6 + - - +
333B ILE* 3.0 5.2 + - + +
334B PHE* 2.8 41.6 + - + -
363B SER* 3.7 27.4 - - - +
367B ILE* 3.9 14.4 - - + -
397B PHE* 3.8 24.9 - - + -
401B LEU* 4.2 9.0 - - + -
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Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ILE* 4.4 9.4 - - - -
289B GLY 3.2 23.4 + - - +
291B MET 3.5 28.5 - - - +
292B THR* 4.6 3.1 + - - +
307B ALA* 3.7 20.2 - - + +
309B HIS* 3.9 10.8 - - + +
328B ASN 4.8 0.4 + - - -
330B ILE* 1.3 75.4 - - - +
332B SER* 1.3 62.6 + - - +
334B PHE* 3.3 3.5 + - - +
335B ALA* 3.0 21.0 + - - +
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Residues in contact with SER 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B THR* 4.5 8.5 + - - +
22B ILE* 4.4 11.1 - - - +
23B TRP* 4.1 17.2 - - - -
26B ILE* 3.6 17.9 - - - -
307B ALA* 3.9 7.7 - - - +
309B HIS* 4.0 20.3 + - - -
328B ASN 5.0 0.3 + - - -
329B PRO* 3.2 12.5 + - - +
331B ALA* 1.3 78.2 - - - +
333B ILE* 1.3 64.2 + - - +
335B ALA* 3.1 19.8 + - - +
336B TRP* 3.4 12.5 - - - -
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Residues in contact with ILE 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ILE* 3.6 20.2 - - + -
30B LEU* 3.6 19.5 - - + -
329B PRO* 2.8 33.9 + - + +
330B ILE* 3.4 13.5 - - + +
332B SER* 1.3 73.4 - - - +
334B PHE* 1.3 60.7 + - + +
336B TRP* 2.9 23.7 + - - +
337B THR* 3.0 14.4 + - + +
359B LEU* 4.0 25.6 - - + -
363B SER* 3.8 17.5 - - - +
398B MET* 4.6 1.6 - - - -
401B LEU* 3.6 31.0 - - + -
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Residues in contact with PHE 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ILE* 3.4 43.5 - - + -
292B THR* 3.9 11.2 - - - +
330B ILE* 2.8 38.9 + - + +
331B ALA 3.8 4.3 - - - +
332B SER 3.3 0.2 - - - -
333B ILE* 1.3 74.7 - - + +
335B ALA* 1.3 60.9 + - - +
337B THR* 3.1 7.9 - - - -
338B ARG* 2.9 61.0 + - - +
360B GLU* 3.5 46.2 - - + -
363B SER* 3.9 19.5 - - - -
364B ILE* 4.4 7.0 - - + -
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Residues in contact with ALA 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B TRP* 4.4 14.1 - - + -
71B VAL* 3.3 12.9 - - + +
292B THR* 4.7 1.5 + - - -
305B ALA* 3.4 15.4 - - - +
306B GLU* 3.6 33.0 - - - +
307B ALA 4.0 1.8 - - - +
331B ALA 3.0 11.7 + - - +
332B SER* 3.1 13.2 + - - +
334B PHE* 1.3 77.6 - - - +
336B TRP* 1.3 61.4 + - - +
339B GLY 3.2 16.8 + - - -
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Residues in contact with TRP 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 4.7 4.3 - - + -
12B GLU* 3.9 15.9 - - + -
23B TRP* 3.2 47.7 - + - -
26B ILE* 3.8 21.8 - - + +
27B LYS* 3.6 37.4 - - + +
31B ILE* 4.1 33.9 - - + -
32B PHE* 5.6 1.3 - + - -
37B LEU* 4.1 23.1 - - + -
39B LEU* 4.7 5.2 - - + -
71B VAL* 4.2 19.6 - - + +
332B SER 3.4 21.7 + - - -
333B ILE* 2.9 9.2 + - + +
335B ALA* 1.3 75.6 - - - +
337B THR* 1.3 59.6 + - + +
339B GLY* 3.3 0.9 + - - -
340B LEU* 2.8 46.9 + - + +
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Residues in contact with THR 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B ILE* 3.0 18.5 + - + +
334B PHE* 3.1 16.5 - - - -
336B TRP* 1.3 76.6 - - - +
338B ARG* 1.3 59.1 + - - +
340B LEU* 4.6 2.9 - - + -
341B ALA* 2.9 30.7 + - - +
356B ALA* 3.6 28.5 - - - +
359B LEU* 3.8 30.5 - - + -
360B GLU* 2.7 39.0 + - + +
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Residues in contact with ARG 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B GLU* 3.3 34.8 + - - -
112B ILE* 5.9 1.6 - - - +
203B LYS* 5.2 5.5 - - - +
292B THR* 3.3 28.7 - - - +
293B SER 6.0 0.4 - - - +
294B VAL* 5.4 16.9 - - + +
303B VAL* 5.3 3.1 - - + +
305B ALA* 4.1 14.8 - - + -
334B PHE* 2.9 45.0 + - - +
335B ALA* 4.9 0.2 - - - -
337B THR* 1.3 78.2 + - - +
339B GLY* 1.3 63.4 + - - +
341B ALA* 3.4 5.5 + - - +
342B HIS* 3.0 23.4 + - - +
360B GLU* 3.1 27.0 + - - -
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Residues in contact with GLY 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B VAL* 3.4 22.3 - - - +
70B GLY 5.0 1.1 - - - -
71B VAL* 4.0 14.6 - - - -
303B VAL* 5.4 3.6 - - - -
305B ALA* 4.2 5.5 - - - +
335B ALA 3.2 16.2 + - - -
336B TRP 3.7 2.7 - - - -
338B ARG* 1.3 76.9 - - - +
340B LEU* 1.3 56.5 + - - +
342B HIS* 3.1 5.2 + - - +
343B ARG* 2.9 24.1 + - - +
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Residues in contact with LEU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 4.0 26.9 - - + -
31B ILE* 4.3 22.2 - - + -
35B VAL* 5.1 1.8 - - + -
37B LEU* 4.1 20.4 - - + -
71B VAL* 6.2 0.7 - - + -
336B TRP* 2.8 33.6 + - + +
337B THR* 4.1 5.4 - - + +
339B GLY* 1.3 71.7 - - - +
341B ALA* 1.3 57.6 + - - +
343B ARG* 3.2 5.2 + - - +
344B ALA* 2.8 31.0 + - - +
352B LEU* 3.5 24.2 - - + +
355B PHE* 4.0 29.4 - - + -
356B ALA* 4.3 7.9 - - + -
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Residues in contact with ALA 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B THR 2.9 19.7 + - - +
338B ARG* 3.7 6.7 - - - +
340B LEU* 1.3 77.4 - - - +
342B HIS* 1.3 55.4 - - - +
344B ALA* 3.3 6.6 + - - +
345B LYS* 3.0 27.8 + - - +
353B ALA* 5.3 4.5 - - - +
356B ALA* 3.9 14.5 - - + +
360B GLU* 5.7 1.8 - - - +
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Residues in contact with HIS 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASN 3.8 7.2 - - - -
69B VAL* 4.0 4.7 - - + -
300B GLY 5.1 2.5 - - - -
301B LYS* 2.7 32.6 + - - -
303B VAL* 3.7 40.5 - - + +
338B ARG 3.0 18.0 + - - +
339B GLY* 3.6 4.3 - - - +
341B ALA* 1.3 74.3 - - - +
343B ARG* 1.3 64.9 + - - +
345B LYS* 3.2 37.5 + - - +
346B LEU* 2.9 51.3 + - + +
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Residues in contact with ARG 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLY 3.3 25.4 - - - +
9B SER* 2.8 51.9 + - - +
10B VAL* 4.3 6.3 - - + -
67B HIS* 3.1 23.2 + - - +
68B ASN* 5.0 3.8 + - - -
69B VAL* 3.7 23.8 - - + +
339B GLY 2.9 14.0 + - - +
340B LEU* 3.4 11.7 - - - +
342B HIS* 1.3 76.1 - - - +
344B ALA* 1.3 62.4 + - - +
346B LEU* 3.3 18.0 + - - +
347B ASP* 2.7 60.3 + - + +
352B LEU* 3.7 7.4 - - + -
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Residues in contact with ALA 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B LEU 2.8 19.9 + - - +
341B ALA 3.7 4.9 - - - +
343B ARG* 1.3 71.3 - - - +
345B LYS* 1.3 57.2 + - - +
348B ASN* 2.7 30.8 + - - -
349B ASN* 2.8 39.5 + - - +
352B LEU* 3.8 8.7 - - + -
353B ALA* 3.5 26.0 - - + +
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Residues in contact with LYS 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B SER* 6.0 1.4 + - - -
300B GLY 5.3 4.8 + - - -
341B ALA 3.0 14.7 + - - +
342B HIS* 3.2 38.1 + - - +
344B ALA* 1.3 76.6 - - - +
346B LEU* 1.3 70.8 + - - +
348B ASN* 3.3 19.6 + - - +
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASN* 3.9 15.9 - - + +
69B VAL* 4.1 5.2 - - + -
300B GLY 5.5 0.7 - - - +
301B LYS* 3.7 39.3 - - + +
342B HIS* 2.9 52.0 + - + +
343B ARG* 3.7 17.7 - - - +
345B LYS* 1.3 84.7 - - - +
347B ASP* 1.3 70.7 + - - +
348B ASN* 3.8 4.3 + - - -
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Residues in contact with ASP 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLY 4.6 3.5 - - - +
8B GLY* 4.8 5.5 - - - -
9B SER 5.1 0.2 + - - -
343B ARG* 2.7 59.4 + - - +
344B ALA 4.4 1.1 - - - +
346B LEU* 1.3 79.4 - - - +
348B ASN* 1.3 70.9 + - - +
349B ASN* 3.4 13.6 + - + +
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Residues in contact with ASN 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B ALA 2.7 14.4 + - - -
345B LYS* 3.3 12.7 + - - +
346B LEU 3.4 3.8 + - - -
347B ASP* 1.3 76.5 - - - +
349B ASN* 1.3 56.6 + - - +
350B LYS* 3.4 7.2 + - - +
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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