Contacts of the helix formed by residues 386 - 403 (chain B) in PDB entry 3DL2
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 ARG 386 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A GLU* 3.0 43.5 + - - +
325B ARG* 5.1 0.2 - - - +
384B GLY* 3.9 6.4 + - - -
385B GLN* 1.3 79.7 - - - +
387B SER* 1.3 66.2 + - - +
388B TRP* 3.3 28.9 - - + +
389B SER* 3.1 17.2 + - - +
390B VAL* 3.1 13.0 + - - +
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Residues in contact with SER 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A GLU* 5.2 3.0 + - - -
192B GLU* 4.0 24.7 + - - +
193B LEU* 3.6 41.2 + - - +
196B ALA* 3.5 8.3 - - - +
385B GLN 4.1 0.2 + - - -
386B ARG* 1.3 72.9 - - - +
388B TRP* 1.3 57.9 + - - +
390B VAL* 3.4 3.5 + - - -
391B GLY 2.8 25.6 + - - -
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Residues in contact with TRP 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A GLY 5.1 1.8 - - - -
191A GLY 5.7 0.2 - - - -
192A GLU* 4.0 27.3 + - + +
195A ILE* 3.6 53.9 - - + +
199A LEU* 5.1 6.5 - - + +
222A ALA 3.4 27.8 - - - -
223A THR* 4.3 4.9 - - - -
225A ASP* 3.7 19.1 - - + -
226A LEU* 4.1 5.4 - - + -
196B ALA* 4.0 12.6 - - + +
386B ARG* 3.7 27.7 - - + +
387B SER* 1.3 76.3 - - - +
389B SER* 1.3 76.6 + - - +
391B GLY* 3.4 1.4 + - - -
392B LEU* 3.1 52.3 + - + +
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Residues in contact with SER 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ASP* 2.5 34.8 + - - +
321B LEU* 4.0 12.5 - - - +
325B ARG* 3.5 14.5 + - - -
386B ARG* 3.1 15.7 + - - +
388B TRP* 1.3 101.3 + - - +
390B VAL* 1.3 65.1 + - - +
392B LEU* 3.3 5.3 + - - +
393B SER* 3.1 21.8 + - - -
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Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 3.7 28.9 - - + -
292B ALA* 4.8 0.4 - - + -
317B ILE* 3.7 30.1 - - + -
321B LEU* 4.2 15.0 - - + -
385B GLN* 4.2 16.8 - - + +
386B ARG 3.1 14.2 + - - +
387B SER* 3.8 2.7 - - - +
389B SER* 1.3 72.5 - - - +
391B GLY* 1.3 60.4 + - - +
393B SER* 2.9 11.0 + - - +
394B VAL* 2.8 40.9 + - + +
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Residues in contact with GLY 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 4.0 0.8 - - - +
196B ALA* 4.0 3.1 - - - -
197B CYS* 3.9 33.1 - - - -
200B ALA* 3.7 8.7 - - - +
387B SER 2.8 16.9 + - - -
388B TRP 3.4 2.9 + - - -
389B SER 3.3 0.2 - - - -
390B VAL* 1.3 77.5 - - - +
392B LEU* 1.3 56.1 + - - +
394B VAL* 3.4 2.1 + - - +
395B ALA* 3.0 29.8 + - - +
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LEU* 4.0 20.0 - - + -
225A ASP* 3.8 26.2 - - + +
226A LEU* 3.9 11.4 - - + +
229A PHE* 3.3 51.2 - - + -
200B ALA* 3.9 13.4 - - + +
388B TRP* 3.1 48.4 + - + +
389B SER 3.6 6.1 - - - +
390B VAL 3.3 0.2 - - - -
391B GLY* 1.3 76.8 - - - +
393B SER* 1.3 60.9 + - - +
395B ALA 3.3 1.0 + - - -
396B ASP* 3.2 18.0 + - - +
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Residues in contact with SER 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ILE* 5.5 2.3 - - - +
320B ASN* 3.6 20.1 + - - +
321B LEU* 4.1 25.5 + - - +
324B GLN* 4.5 7.6 - - - -
389B SER 3.1 11.0 + - - -
390B VAL* 2.9 25.8 + - - +
392B LEU* 1.3 73.4 - - - +
394B VAL* 1.3 66.3 + - - +
396B ASP* 3.4 7.5 + - - +
397B MET* 3.2 30.9 + - - +
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Residues in contact with VAL 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B CYS* 3.8 27.1 - - + -
201B ILE* 5.1 0.7 - - + -
250B ILE* 3.9 28.7 - - + -
290B LEU* 4.1 9.9 - - + -
292B ALA* 4.3 7.4 - - + -
317B ILE* 3.8 26.7 - - + -
390B VAL* 2.8 30.8 + - + +
391B GLY 3.6 4.3 - - - +
393B SER* 1.3 78.2 + - - +
395B ALA* 1.3 65.0 + - - +
397B MET* 3.1 11.2 + - + +
398B VAL* 2.9 21.8 + - + +
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Residues in contact with ALA 395 (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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229A PHE* 3.7 13.5 - - + -
200B ALA* 3.7 20.0 - - + -
201B ILE* 3.7 29.6 - - + +
206B ILE* 3.4 13.3 - - + +
391B GLY 3.0 17.2 + - - +
392B LEU 3.3 5.6 + - - +
394B VAL* 1.3 76.4 - - - +
396B ASP* 1.3 57.7 + - - +
398B VAL* 3.4 3.1 + - - +
399B ASP 2.9 23.4 + - - -
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Residues in contact with ASP 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PHE* 4.0 15.9 - - + -
204B LYS* 5.7 4.0 - - - -
206B ILE* 5.3 0.2 - - - -
324B GLN* 2.9 23.0 + - - +
392B LEU 3.2 13.3 + - - +
393B SER* 3.6 11.0 - - - +
394B VAL 3.2 0.2 - - - -
395B ALA* 1.3 74.5 - - - +
397B MET* 1.3 63.6 + - - +
399B ASP* 3.2 11.0 - - - +
400B SER* 3.1 22.6 + - - -
405B LYS* 4.5 11.4 + - - -
407B LYS* 2.7 32.1 + - - -
409B HIS* 3.3 5.9 - - - -
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Residues in contact with MET 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LEU* 4.3 20.6 - - + -
317B ILE* 3.5 35.4 - - + -
320B ASN* 3.6 18.8 - - + +
393B SER* 3.2 25.6 + - - +
394B VAL* 3.1 15.5 + - + +
396B ASP* 1.3 73.0 - - - +
398B VAL* 1.3 65.5 + - - +
400B SER* 3.2 4.2 + - - -
401B ILE* 3.0 28.8 + - + +
409B HIS* 3.7 29.8 - - + +
411B VAL* 3.6 26.7 - - - -
433B LEU* 4.4 7.5 - - + +
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Residues in contact with VAL 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ILE* 3.5 36.6 - - + -
201B ILE* 4.4 5.8 - - + -
206B ILE* 3.8 8.7 - - + -
248B VAL* 4.3 7.4 - - + -
250B ILE* 3.7 28.9 - - + -
290B LEU* 4.0 12.6 - - + -
394B VAL* 2.9 19.3 + - + +
395B ALA* 3.6 9.6 - - - +
397B MET* 1.3 71.2 - - - +
399B ASP* 1.3 61.2 + - - +
401B ILE* 3.3 7.2 + - - -
402B VAL* 2.9 36.5 + - + +
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Residues in contact with ASP 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LYS* 4.5 13.9 - - - +
206B ILE* 3.9 27.2 - - + +
395B ALA 2.9 13.4 + - - +
396B ASP* 3.2 17.3 - - - +
398B VAL* 1.3 76.7 - - - +
400B SER* 1.3 62.8 + - - +
403B ASN* 2.8 47.8 + - - +
405B LYS* 3.1 30.5 + - - +
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Residues in contact with SER 400 (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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396B ASP 3.1 7.5 + - - -
397B MET 3.2 6.9 + - - -
399B ASP* 1.3 78.0 - - - +
401B ILE* 1.3 56.4 + - - +
404B ASN* 3.1 7.6 + - - -
405B LYS* 2.8 43.9 + - - +
407B LYS* 3.6 16.7 - - - +
409B HIS* 2.7 38.0 + - - -
433B LEU* 3.7 14.3 - - - +
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Residues in contact with ILE 401 (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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247B LYS* 4.1 9.9 - - - +
248B VAL* 3.9 23.6 - - + -
288B VAL* 4.0 36.6 - - + -
290B LEU* 4.8 9.9 - - + -
315B ILE* 4.3 16.2 - - + -
397B MET 3.0 26.1 + - - +
398B VAL* 3.3 7.4 + - - +
400B SER* 1.3 76.8 - - - +
402B VAL* 1.3 64.7 + - - +
404B ASN 3.2 9.5 + - - -
433B LEU* 4.3 15.9 - - + -
434B GLY 3.3 21.8 - - - +
435B THR* 3.3 22.2 + - - +
437B GLY* 5.1 2.5 - - - -
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Residues in contact with VAL 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ASN* 3.9 33.5 + - + +
185B ILE* 4.3 10.3 - - + -
206B ILE* 3.8 25.8 - - + +
247B LYS* 3.9 17.0 - - + +
248B VAL* 3.8 25.4 - - + -
398B VAL* 2.9 33.8 + - + +
401B ILE* 1.3 71.7 - - - +
403B ASN* 1.3 77.1 + - - +
404B ASN 3.4 1.0 + - - -
435B THR* 4.3 7.8 - - - +
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Residues in contact with ASN 403 (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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183B ASN* 4.8 5.7 + - - -
206B ILE* 4.8 5.4 + - - +
399B ASP* 2.8 38.7 + - - +
402B VAL* 1.3 91.8 + - - +
404B ASN* 1.3 71.4 + - - +
405B LYS* 3.2 13.6 + - + +
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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
------------------------------------------------------------
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