Contacts of the helix formed by residues 321 - 342 (chain L) in PDB entry 3Q2K
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 ASP 321 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126L LEU 3.3 13.9 - - - +
128L VAL* 4.1 3.5 - - - +
318L PRO* 3.8 28.2 - - + +
319L GLU 3.9 4.8 - - - +
320L THR* 1.3 77.4 - - - +
322L GLY* 1.3 60.3 + - - +
323L ARG* 4.1 20.7 + - - +
324L GLU* 2.9 32.2 + - - +
325L GLY* 3.0 9.0 + - - -
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Residues in contact with GLY 322 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105L MET* 3.4 14.9 - - - +
116L VAL* 3.8 10.5 - - - -
126L LEU* 3.2 38.6 + - - +
128L VAL* 4.4 2.9 - - - -
321L ASP* 1.3 72.1 - - - +
323L ARG* 1.3 64.5 + - - +
325L GLY 3.3 7.6 + - - -
326L LEU* 3.3 11.6 + - - +
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Residues in contact with ARG 323 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179I GLU* 2.7 44.0 + - - +
180I TRP* 4.0 20.5 - - - +
116L VAL* 4.1 16.2 - - + +
120L ASP* 2.9 38.8 + - - -
321L ASP* 3.3 15.8 + - - +
322L GLY* 1.3 73.5 - - - +
324L GLU* 1.3 66.8 + - - +
326L LEU* 3.0 29.5 + - + +
327L GLN* 3.2 20.0 + - - +
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Residues in contact with GLU 324 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130L LYS* 3.9 5.6 + - - -
133L ARG* 3.4 34.1 + - - +
197L ASP* 5.3 3.7 - - - +
198L TRP* 4.6 5.0 - - - -
319L GLU 3.9 10.2 - - - +
320L THR* 3.5 22.9 - - + -
321L ASP* 2.9 30.5 + - - +
323L ARG* 1.3 77.9 - - - +
325L GLY* 1.3 58.7 - - - +
327L GLN* 3.2 29.0 + - - +
328L SER 3.9 2.3 + - - -
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Residues in contact with GLY 325 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105L MET* 3.2 24.6 + - - +
128L VAL* 4.3 10.1 - - - -
130L LYS* 4.2 16.6 - - - -
320L THR* 4.3 0.6 - - - +
321L ASP 3.0 12.1 + - - -
322L GLY 3.3 1.0 + - - -
323L ARG 3.2 0.6 - - - -
324L GLU* 1.3 76.7 - - - +
326L LEU* 1.3 56.5 + - - +
327L GLN 3.2 0.2 - - - -
328L SER* 3.4 6.7 + - - -
329L LEU* 3.1 21.3 + - - +
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Residues in contact with LEU 326 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105L MET* 3.9 6.5 - - + -
109L TRP* 3.7 26.7 - - + -
112L GLY* 3.4 37.7 - - - +
113L LYS* 3.7 9.4 - - + +
116L VAL* 3.8 20.9 - - + -
322L GLY 3.3 15.1 + - - +
323L ARG* 3.0 21.1 + - + +
325L GLY* 1.3 74.7 - - - +
327L GLN* 1.3 63.9 + - - +
329L LEU* 3.7 5.6 - - + -
330L ALA* 2.7 32.6 + - - +
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Residues in contact with GLN 327 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218I GLU* 4.9 13.7 + - - +
133L ARG* 6.0 0.7 - - - +
197L ASP* 3.3 41.4 + - + +
323L ARG* 3.2 18.9 + - - +
324L GLU* 3.2 23.4 + - - +
325L GLY 3.2 0.4 - - - -
326L LEU* 1.3 83.8 - - - +
328L SER* 1.3 61.4 + - - +
330L ALA* 3.4 6.3 + - - +
331L LEU* 3.3 18.4 + - - +
347L LEU* 6.1 0.2 - - - +
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Residues in contact with SER 328 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104L PRO* 6.1 1.2 - - - +
130L LYS* 3.1 28.1 + - - +
190L SER 5.2 2.4 + - - -
193L VAL* 4.4 3.9 - - - +
194L ASP* 4.1 25.7 - - - +
197L ASP* 6.1 1.8 - - - -
324L GLU 3.9 1.2 + - - -
325L GLY 3.4 6.6 + - - -
326L LEU 3.2 0.2 - - - -
327L GLN* 1.3 80.0 - - - +
329L LEU* 1.3 61.1 + - - +
331L LEU* 3.3 9.4 + - - +
332L LEU* 2.8 37.6 + - - +
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Residues in contact with LEU 329 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104L PRO* 5.4 2.7 - - + -
105L MET* 4.2 13.5 - - + +
106L ALA* 3.4 26.7 - - + +
107L THR 4.5 0.7 - - - +
108L ARG 3.8 24.0 - - - +
109L TRP* 4.0 17.0 - - + -
112L GLY* 3.8 22.4 - - - -
186L MET* 4.5 15.3 - - + -
325L GLY 3.1 15.7 + - - +
326L LEU* 4.0 9.9 - - + +
327L GLN 3.4 0.2 - - - -
328L SER* 1.3 82.3 + - - +
330L ALA* 1.3 55.8 + - - +
332L LEU* 3.4 8.9 + - + +
333L THR* 2.8 41.2 + - - +
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Residues in contact with ALA 330 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109L TRP* 3.6 25.1 - - + -
326L LEU 2.7 22.1 + - - +
327L GLN* 3.7 7.9 - - - +
329L LEU* 1.3 68.2 - - - +
331L LEU* 1.3 61.9 + - - +
333L THR* 3.2 1.4 + - - -
334L ALA* 2.8 31.4 + - - +
347L LEU* 4.2 14.1 - - + -
348L PRO* 6.3 0.2 - - + -
349L LEU* 3.8 16.4 - - + +
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Residues in contact with LEU 331 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193L VAL* 3.8 14.1 - - + +
196L LEU* 3.6 41.3 - - + -
197L ASP* 4.6 10.3 - - + +
203L VAL* 4.1 20.6 - - + -
206L VAL* 3.8 27.6 - - + -
227L LEU* 4.7 1.1 - - + -
327L GLN 3.3 10.4 + - - +
328L SER* 3.3 10.5 + - - +
330L ALA* 1.3 78.7 - - - +
332L LEU* 1.3 63.8 + - - +
334L ALA* 3.3 3.5 + - - +
335L ILE* 3.0 34.3 + - + +
347L LEU* 4.6 8.6 - - + +
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Residues in contact with LEU 332 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104L PRO* 4.7 9.6 - - + -
185L PHE* 3.5 38.1 - - + +
186L MET* 3.9 43.1 - - + +
190L SER* 4.5 9.4 - - - -
193L VAL* 3.8 23.8 - - + -
328L SER* 2.8 28.0 + - - +
329L LEU* 3.7 11.0 - - + +
331L LEU* 1.3 72.3 - - - +
333L THR* 1.3 65.4 + - - +
335L ILE* 3.0 7.2 + - + +
336L TYR* 2.8 28.3 + - + +
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Residues in contact with THR 333 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107L THR 5.6 0.9 + - - -
108L ARG* 5.5 0.2 - - - -
109L TRP* 3.6 28.0 + - + +
186L MET* 5.8 1.9 - - - +
329L LEU* 2.8 29.1 + - - +
330L ALA 3.5 4.9 - - - -
332L LEU* 1.3 74.6 - - - +
334L ALA* 1.3 54.4 + - - +
336L TYR* 3.0 10.0 + - - +
337L ARG* 2.7 63.2 + - + +
349L LEU* 3.6 19.3 - - + -
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Residues in contact with ALA 334 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206L VAL* 4.0 13.0 - - + -
330L ALA 2.8 17.1 + - - +
331L LEU* 3.4 7.2 - - - +
333L THR* 1.3 79.8 - - - +
335L ILE* 1.3 61.5 + - - +
337L ARG* 3.3 1.5 + - - +
338L SER* 3.0 25.1 + - - -
345L ILE* 3.7 32.4 - - + +
347L LEU* 4.2 18.8 - - + -
349L LEU* 4.6 2.0 - - + -
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Residues in contact with ILE 335 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185L PHE* 3.9 41.1 - - + -
193L VAL* 4.5 9.4 - - + -
196L LEU* 5.5 0.4 - - + -
206L VAL* 3.8 21.1 - - + -
208L ALA* 3.6 19.0 - - + +
210L THR* 4.7 2.5 - - + -
225L ALA* 4.2 11.9 - - + -
227L LEU* 5.5 0.4 - - + -
237L ILE* 5.0 4.0 - - + -
331L LEU* 3.0 35.8 + - + +
332L LEU* 3.3 11.2 - - + +
334L ALA* 1.3 75.5 - - - +
336L TYR* 1.3 72.3 + - + +
338L SER* 3.6 1.6 - - - -
339L ALA* 2.9 27.5 + - - +
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Residues in contact with TYR 336 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107L THR 5.7 1.1 - - - -
178L TRP* 4.0 24.0 - + - -
182L GLY* 4.3 3.8 - - - -
183L GLY 3.0 16.6 + - - -
185L PHE* 3.9 16.8 - + + -
186L MET* 3.3 45.4 + - + +
210L THR* 5.2 5.4 - - + -
220L GLU* 2.4 40.8 + - - -
332L LEU* 2.8 17.4 + - + +
333L THR* 3.4 9.9 - - - +
335L ILE* 1.3 84.8 - - + +
337L ARG* 1.3 57.2 + - + +
339L ALA* 3.9 3.5 - - + +
340L ARG* 3.0 28.8 + - - +
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Residues in contact with ARG 337 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109L TRP* 4.0 23.0 - - - +
333L THR* 2.7 38.3 + - + +
334L ALA* 3.8 3.8 - - - +
336L TYR* 1.3 70.4 - - - +
338L SER* 1.3 58.2 + - - +
340L ARG* 4.2 20.8 - - - +
341L ASP* 2.7 44.5 + - - +
345L ILE* 3.9 25.7 - - + +
349L LEU* 3.8 27.3 - - - +
350L ASP* 5.3 4.0 + - - +
350N ASP* 4.9 13.6 + - - +
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Residues in contact with SER 338 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206L VAL* 4.3 2.7 - - - -
207L TYR* 3.3 11.3 - - - -
208L ALA* 2.9 30.6 + - - +
334L ALA 3.0 17.4 + - - -
335L ILE* 3.6 3.8 - - - -
337L ARG* 1.3 77.6 - - - +
339L ALA* 1.3 61.9 + - - +
342L GLY* 2.7 30.1 + - - -
343L VAL 2.7 26.7 + - - +
345L ILE* 3.6 8.3 - - - +
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Residues in contact with ALA 339 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228K ARG* 5.9 1.2 + - - -
208L ALA 3.3 15.9 + - - +
209L TYR* 4.7 1.5 - - - +
210L THR* 3.4 43.8 - - + +
335L ILE 2.9 17.9 + - - +
336L TYR* 4.0 5.4 - - + +
338L SER* 1.3 78.6 - - - +
340L ARG* 1.3 62.8 + - - +
342L GLY* 4.0 4.2 + - - -
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Residues in contact with ARG 340 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336L TYR 3.0 19.4 + - - +
337L ARG* 3.8 17.6 - - - +
339L ALA* 1.3 81.8 - - - +
341L ASP* 1.3 90.8 + - - +
342L GLY 3.7 0.2 + - - -
344N ARG* 5.2 2.8 + - - -
346N PRO* 3.5 28.2 - - + +
347N LEU 3.7 19.5 - - - +
348N PRO* 3.3 35.9 + - + +
349N LEU* 4.0 1.0 - - - +
350N ASP* 2.6 49.2 + - - +
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Residues in contact with ASP 341 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337L ARG* 2.7 27.4 + - - +
340L ARG* 1.3 115.5 + - - +
342L GLY* 1.3 62.8 + - - +
343L VAL* 3.3 23.8 + - + +
345L ILE* 5.2 2.1 - - - +
344N ARG* 4.0 14.8 + - - +
346N PRO* 3.4 15.6 - - - +
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Residues in contact with GLY 342 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344K ARG* 3.4 27.6 + - - +
207L TYR* 3.4 23.3 + - - -
208L ALA 5.6 0.2 - - - -
338L SER 2.7 19.1 + - - -
339L ALA 4.0 4.0 + - - -
340L ARG 3.5 2.4 - - - -
341L ASP* 1.3 72.3 - - - +
343L VAL* 1.3 60.5 + - - +
344N ARG* 5.1 2.9 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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