Contacts of the helix formed by residues 386 - 403 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ARG* 5.0 0.2 - - - +
384A GLY* 3.9 5.5 - - - -
385A GLN* 1.3 79.3 - - - +
387A SER* 1.3 66.6 + - - +
388A TRP* 3.3 28.9 - - + +
389A SER* 3.1 11.0 + - - +
390A VAL* 3.1 19.7 + - - +
192B GLU* 4.0 16.8 - - + +
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Residues in contact with SER 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A GLU* 4.1 23.2 + - - +
193A LEU* 3.7 39.7 + - - +
196A ALA* 3.5 9.3 - - - +
386A ARG* 1.3 73.3 - - - +
388A TRP* 1.3 56.5 + - - +
390A VAL* 3.3 4.1 + - - -
391A GLY 2.8 25.3 + - - -
192B GLU* 5.0 3.6 + - - -
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Residues in contact with TRP 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ALA* 4.0 11.9 - - + +
386A ARG* 3.8 24.1 - - + +
387A SER* 1.3 78.4 - - - +
389A SER* 1.3 79.4 + - - +
391A GLY* 3.3 1.0 + - - -
392A LEU* 3.0 59.1 + - + +
190B GLY 5.0 2.2 - - - -
191B GLY 5.6 0.4 - - - -
192B GLU* 3.9 29.5 + - + +
195B ILE* 3.7 52.3 - - + +
199B LEU* 5.1 6.1 - - + +
222B ALA 3.3 28.0 - - - -
223B THR* 4.3 5.4 - - - -
225B ASP* 3.7 19.7 - - + -
226B LEU* 4.1 5.6 - - + -
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Residues in contact with SER 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU* 4.0 13.0 - - - +
325A ARG* 3.4 15.6 + - - -
386A ARG* 3.1 14.7 + - - +
388A TRP* 1.3 102.2 + - - +
390A VAL* 1.3 61.3 + - - +
392A LEU* 3.3 5.2 + - - +
393A SER* 3.1 22.3 + - - -
225B ASP* 2.5 34.3 + - - +
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Residues in contact with VAL 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 3.7 25.6 - - + -
292A ALA* 4.8 0.4 - - + +
317A ILE* 3.7 30.7 - - + -
321A LEU* 4.1 14.6 - - + -
385A GLN* 4.1 18.2 - - + +
386A ARG 3.1 15.0 + - - +
387A SER* 3.8 6.7 - - - +
389A SER* 1.3 72.8 - - - +
391A GLY* 1.3 59.9 + - - +
393A SER* 2.9 9.9 + - - +
394A VAL* 2.9 35.9 + - + +
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Residues in contact with GLY 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 4.0 0.8 - - - +
196A ALA* 4.0 3.1 - - - -
197A CYS* 3.9 34.3 - - - -
200A ALA* 3.7 9.1 - - - +
387A SER 2.8 19.8 + - - -
388A TRP 3.7 2.0 - - - -
389A SER 3.3 0.2 - - - -
390A VAL* 1.3 75.0 - - - +
392A LEU* 1.3 55.8 + - - +
394A VAL* 3.4 2.1 + - - +
395A ALA* 3.0 28.8 + - - +
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Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ALA* 3.8 14.8 - - + +
388A TRP* 3.0 48.7 + - + +
389A SER 3.6 5.8 - - - +
390A VAL 3.3 0.2 - - - -
391A GLY* 1.3 75.3 - - - +
393A SER* 1.3 63.1 + - - +
395A ALA 3.3 1.0 + - - -
396A ASP* 3.2 18.0 + - - +
199B LEU* 4.0 19.5 - - + -
225B ASP* 3.8 26.5 - - + +
226B LEU* 3.9 11.9 - - + +
229B PHE* 3.3 51.0 - - + -
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Residues in contact with SER 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ILE* 5.5 2.9 - - - +
320A ASN* 3.6 23.6 + - - +
321A LEU* 4.1 25.5 + - - +
324A GLN* 4.6 7.6 - - - -
389A SER 3.1 12.0 + - - -
390A VAL* 2.9 24.9 + - - +
392A LEU* 1.3 75.9 - - - +
394A VAL* 1.3 61.7 + - - +
396A ASP* 3.4 7.2 + - - +
397A MET* 3.2 29.4 + - - +
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Residues in contact with VAL 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A CYS* 3.8 28.7 - - + -
201A ILE* 5.0 0.7 - - + -
250A ILE* 3.9 29.6 - - + -
290A LEU* 4.2 7.0 - - + -
292A ALA* 4.3 7.6 - - + -
317A ILE* 3.8 27.6 - - + -
390A VAL* 2.9 28.7 + - + +
391A GLY 3.6 4.3 - - - +
393A SER* 1.3 78.2 + - - +
395A ALA* 1.3 62.7 + - - +
397A MET* 3.1 11.0 + - + +
398A VAL* 2.9 22.7 + - + +
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Residues in contact with ALA 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ALA* 3.7 15.7 - - + +
201A ILE* 3.7 27.1 - - + +
206A ILE* 3.4 15.4 - - + +
391A GLY 3.0 17.6 + - - +
392A LEU 3.3 5.4 + - - +
394A VAL* 1.3 77.1 - - - +
396A ASP* 1.3 57.1 - - - +
398A VAL* 3.4 3.2 + - - +
399A ASP 2.9 23.2 + - - -
229B PHE* 3.7 17.0 - - + -
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Residues in contact with ASP 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LYS* 4.7 9.3 + - - +
206A ILE* 5.4 0.2 - - - -
324A GLN* 2.8 25.2 + - - +
392A LEU 3.2 10.2 + - - +
393A SER 3.6 9.4 - - - +
394A VAL 3.2 0.8 - - - -
395A ALA* 1.3 76.7 - - - +
397A MET* 1.3 63.7 + - - +
399A ASP* 3.2 11.0 - - - +
400A SER* 3.1 22.5 + - - -
405A LYS* 4.5 11.6 + - - -
407A LYS* 2.7 34.2 + - - +
409A HIS* 3.2 7.0 - - - -
229B PHE* 4.1 11.8 - - + -
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Residues in contact with MET 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LEU* 4.3 20.6 - - + -
317A ILE* 3.5 35.7 - - + -
320A ASN* 3.6 24.5 - - + +
393A SER* 3.2 24.1 + - - +
394A VAL* 3.1 16.2 + - + +
396A ASP* 1.3 72.9 - - - +
398A VAL* 1.3 63.7 + - - +
400A SER* 3.3 4.2 + - - -
401A ILE* 3.1 30.0 + - + +
409A HIS* 3.6 23.3 - - + +
411A VAL* 3.7 26.2 - - - -
433A LEU* 4.5 7.9 - - + +
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Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ILE* 3.5 36.1 - - + -
201A ILE* 4.3 6.3 - - + -
206A ILE* 3.9 9.0 - - + -
248A VAL* 4.3 8.3 - - + -
250A ILE* 3.7 28.9 - - + -
290A LEU* 4.1 13.0 - - + -
394A VAL* 2.9 20.0 + - + +
395A ALA* 3.6 9.0 - - - +
397A MET* 1.3 73.3 - - - +
399A ASP* 1.3 60.9 + - - +
401A ILE* 3.2 7.2 + - - -
402A VAL* 2.9 37.4 + - + +
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Residues in contact with ASP 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LYS* 4.4 15.8 + - - +
206A ILE* 3.9 26.9 - - + +
395A ALA 2.9 13.9 + - - +
396A ASP* 3.2 15.8 - - - +
398A VAL* 1.3 75.8 - - - +
400A SER* 1.3 61.6 + - - +
403A ASN* 2.8 55.3 + - - +
405A LYS* 3.3 29.2 + - - +
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Residues in contact with SER 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ASP* 3.1 6.4 + - - -
397A MET 3.3 7.1 + - - -
399A ASP* 1.3 76.9 - - - +
401A ILE* 1.3 57.5 + - - +
404A ASN* 3.1 8.7 + - - -
405A LYS* 2.8 43.4 + - - +
407A LYS* 3.6 17.3 - - - +
409A HIS* 2.7 37.9 + - - -
433A LEU* 3.8 15.1 - - - +
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Residues in contact with ILE 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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247A LYS* 5.0 2.0 - - + +
248A VAL* 3.9 20.4 - - + -
288A VAL* 3.8 41.7 - - + -
290A LEU* 4.8 10.1 - - + -
315A ILE* 4.4 15.9 - - + -
397A MET 3.1 21.5 + - - +
398A VAL* 3.2 8.7 + - - +
400A SER* 1.3 75.6 - - - +
402A VAL* 1.3 63.2 + - + +
404A ASN 3.2 10.0 + - - -
433A LEU* 4.4 15.0 - - + -
434A GLY 3.3 22.2 - - - +
435A THR* 3.4 24.5 + - - +
437A GLY* 5.2 2.5 - - - -
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Residues in contact with VAL 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ASN* 3.8 32.9 + - + +
185A ILE* 4.2 11.4 - - + -
206A ILE* 3.8 25.4 - - + +
247A LYS* 4.5 11.2 - - + -
248A VAL* 3.8 24.7 - - + -
398A VAL* 2.9 33.8 + - + +
401A ILE* 1.3 73.5 - - + +
403A ASN* 1.3 79.1 + - - +
404A ASN* 3.8 0.7 + - - +
435A THR* 5.4 4.6 + - - +
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Residues in contact with ASN 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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183A ASN* 4.7 4.7 - - - +
206A ILE* 4.8 6.7 + - - +
399A ASP* 2.8 42.2 + - - +
402A VAL* 1.3 92.8 - - - +
404A ASN* 1.3 71.1 + - - +
405A LYS* 3.2 13.4 + - + +
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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