Contacts of the helix formed by residues 321 - 342 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126P LEU 3.2 15.3 - - - +
128P VAL* 4.1 3.1 - - - +
317P GLU* 5.5 1.4 - - - +
318P PRO* 3.7 32.6 - - + +
319P GLU 4.0 1.1 - - - +
320P THR* 1.3 80.1 - - - +
322P GLY* 1.3 65.5 + - - +
323P ARG* 4.0 14.9 + - - +
324P GLU* 3.2 25.5 + - - +
325P GLY 3.2 8.3 + - - -
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Residues in contact with GLY 322 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105P MET* 3.6 8.6 - - - +
116P VAL* 4.0 9.6 - - - -
126P LEU* 3.0 37.1 + - - +
128P VAL* 4.1 8.1 - - - -
321P ASP* 1.3 76.4 - - - +
323P ARG* 1.3 57.2 + - - +
325P GLY* 2.9 17.3 + - - -
326P LEU* 3.0 11.4 + - - +
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Residues in contact with ARG 323 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179J GLU* 2.8 42.9 + - - +
180J TRP* 3.7 25.9 - - - +
116P VAL* 3.6 21.0 - - + +
120P ASP* 2.7 40.8 + - - -
321P ASP* 3.3 13.5 + - - +
322P GLY* 1.3 74.7 - - - +
324P GLU* 1.3 64.0 + - - +
326P LEU* 3.3 23.9 + - + +
327P GLN* 3.5 15.4 + - - +
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Residues in contact with GLU 324 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130P LYS* 3.7 8.3 + - - +
133P ARG* 3.0 43.9 + - - +
197P ASP* 4.8 6.4 - - - +
198P TRP* 4.7 3.8 - - - -
319P GLU 4.5 4.5 - - - +
320P THR* 4.0 16.4 - - + +
321P ASP* 3.2 29.6 + - - +
323P ARG* 1.3 76.8 - - - +
325P GLY* 1.3 62.4 + - - +
327P GLN* 3.1 29.4 + - - +
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Residues in contact with GLY 325 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105P MET* 3.4 21.7 - - - +
128P VAL* 4.5 13.2 - - - -
130P LYS* 3.8 13.0 - - - +
320P THR* 4.6 0.8 - - - +
321P ASP 3.2 5.1 + - - -
322P GLY 2.9 9.7 + - - -
324P GLU* 1.3 80.5 - - - +
326P LEU* 1.3 60.4 + - - +
328P SER* 3.3 5.4 + - - -
329P LEU* 3.2 18.0 + - - +
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Residues in contact with LEU 326 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105P MET* 3.6 10.5 - - + -
109P TRP* 3.6 28.6 - - + -
112P GLY* 3.7 32.5 - - - +
113P LYS* 3.8 14.8 - - + +
116P VAL* 4.1 14.1 - - + -
322P GLY 3.0 13.2 + - - +
323P ARG* 3.5 20.0 - - + +
324P GLU 3.2 0.8 - - - -
325P GLY* 1.3 73.4 - - - +
327P GLN* 1.3 68.7 + - - +
329P LEU* 4.3 4.3 - - + -
330P ALA* 2.9 28.4 + - - +
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Residues in contact with GLN 327 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218J GLU* 4.0 16.6 + - - +
133P ARG* 5.9 1.3 - - - +
197P ASP* 3.3 39.9 - - - +
323P ARG 3.5 9.2 + - - +
324P GLU* 3.1 25.0 + - - +
326P LEU* 1.3 83.5 + - - +
328P SER* 1.3 63.1 + - - +
330P ALA* 3.6 7.7 + - - +
331P LEU* 3.3 19.1 + - - +
347P LEU* 6.0 0.5 - - - +
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Residues in contact with SER 328 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130P LYS* 2.8 34.0 + - - -
190P SER 5.5 1.3 - - - -
193P VAL* 4.7 2.8 - - - +
194P ASP* 4.2 23.6 - - - -
197P ASP* 5.8 3.6 - - - +
324P GLU 3.7 1.4 + - - -
325P GLY* 3.3 5.8 + - - -
327P GLN* 1.3 81.0 - - - +
329P LEU* 1.3 60.8 + - - +
331P LEU* 3.3 7.2 + - - +
332P LEU* 2.9 40.9 + - - +
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Residues in contact with LEU 329 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104P PRO* 5.6 3.1 - - + -
105P MET* 4.2 12.6 - - + +
106P ALA* 3.6 29.6 - - + +
107P THR 4.4 11.9 - - - +
108P ARG 4.0 10.8 - - - +
109P TRP* 4.1 16.6 - - + -
112P GLY* 3.9 28.0 - - - -
186P MET* 4.5 10.3 - - + -
325P GLY 3.2 13.4 + - - +
326P LEU* 3.3 8.0 + - + +
328P SER* 1.3 81.8 + - - +
330P ALA* 1.3 50.8 + - - +
332P LEU* 3.5 9.9 + - + +
333P THR* 2.6 45.1 + - - +
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Residues in contact with ALA 330 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109P TRP* 3.4 26.6 - - + -
326P LEU 2.9 17.8 + - - +
327P GLN* 3.8 9.4 - - - +
329P LEU* 1.3 74.2 - - - +
331P LEU* 1.3 57.5 + - - +
333P THR* 3.1 1.9 + - - -
334P ALA* 2.8 30.5 + - - +
347P LEU* 4.1 10.5 - - + +
348P PRO* 6.3 0.2 - - + -
349P LEU* 3.6 20.6 - - + +
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Residues in contact with LEU 331 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193P VAL* 3.7 33.9 - - + +
196P LEU* 4.0 22.0 - - + -
197P ASP* 4.9 9.4 - - + +
203P VAL* 4.1 18.8 - - + -
206P VAL* 3.7 27.4 - - + -
227P LEU* 5.3 2.0 - - + -
327P GLN 3.3 10.7 + - - +
328P SER* 3.3 9.8 + - - +
329P LEU 3.3 0.6 - - - -
330P ALA* 1.3 75.7 - - - +
332P LEU* 1.3 64.8 + - - +
334P ALA* 3.2 3.2 + - + +
335P ILE* 3.0 32.5 + - + +
347P LEU* 4.0 20.4 - - + +
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Residues in contact with LEU 332 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104P PRO* 5.0 8.5 - - + -
185P PHE* 3.6 37.9 - - + +
186P MET* 3.9 35.2 - - + +
190P SER* 4.5 13.7 - - - +
193P VAL* 4.0 26.0 - - + -
328P SER* 2.9 31.4 + - - +
329P LEU* 3.7 9.6 - - + +
331P LEU* 1.3 75.0 - - - +
333P THR* 1.3 57.3 + - - +
335P ILE* 3.2 9.7 + - + +
336P TYR* 2.9 34.8 + - + +
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Residues in contact with THR 333 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107P THR 5.6 0.5 + - - -
109P TRP* 3.5 33.1 + - + +
186P MET* 5.8 1.9 - - - +
329P LEU* 2.6 35.4 + - - +
330P ALA* 3.1 5.3 + - - -
332P LEU* 1.3 74.3 - - - +
334P ALA* 1.3 59.6 + - - +
336P TYR* 3.2 6.1 + - + +
337P ARG* 2.8 65.9 + - + +
349P LEU* 4.0 8.5 - - + -
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Residues in contact with ALA 334 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206P VAL* 3.7 14.8 - - + -
330P ALA 2.8 16.9 + - - +
331P LEU* 3.6 6.7 - - - +
332P LEU 3.2 0.2 - - - -
333P THR* 1.3 78.7 - - - +
335P ILE* 1.3 56.6 + - - +
337P ARG* 4.5 0.7 - - - -
338P SER* 2.9 30.5 + - - -
345P ILE* 3.5 31.9 - - + +
347P LEU* 4.1 19.1 - - + -
349P LEU* 4.4 2.9 - - + +
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Residues in contact with ILE 335 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185P PHE* 4.0 40.4 - - + -
193P VAL* 4.6 13.9 - - + -
196P LEU* 5.5 0.7 - - + -
206P VAL* 4.0 17.0 - - + -
208P ALA* 3.7 17.9 - - + +
210P THR* 4.8 2.9 - - + -
225P ALA* 3.9 17.5 - - + -
227P LEU* 5.3 1.8 - - + -
237P ILE* 5.0 3.8 - - + -
331P LEU* 3.0 27.7 + - + +
332P LEU* 3.5 11.4 - - + +
334P ALA* 1.3 76.4 - - - +
336P TYR* 1.3 68.8 + - + +
338P SER* 3.3 2.3 + - - -
339P ALA* 3.0 28.4 + - - +
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Residues in contact with TYR 336 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178P TRP* 4.1 27.1 - + + -
182P GLY* 4.4 2.7 - - - -
183P GLY 2.9 17.8 + - - -
185P PHE* 3.6 15.7 - + + -
186P MET* 3.1 48.2 + - + -
210P THR* 5.1 6.1 - - + -
220P GLU* 2.5 41.1 + - - -
332P LEU* 2.9 18.8 + - + +
333P THR* 4.0 5.4 - - + +
335P ILE* 1.3 84.5 - - + +
337P ARG* 1.3 61.8 + - - +
339P ALA* 3.6 4.6 + - + +
340P ARG* 3.1 24.6 + - - +
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Residues in contact with ARG 337 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350M ASP* 4.6 18.3 + - - +
109P TRP* 3.8 26.5 - - - +
333P THR* 2.8 37.9 + - + +
334P ALA* 3.9 4.0 - - - +
336P TYR* 1.3 74.9 - - - +
338P SER* 1.3 59.2 + - - +
340P ARG* 3.4 19.9 + - - +
341P ASP* 2.9 40.1 + - - +
345P ILE* 3.9 24.7 - - + +
349P LEU* 4.0 23.7 - - - +
350P ASP* 5.3 4.6 + - - +
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Residues in contact with SER 338 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206P VAL* 4.2 4.5 - - - -
207P TYR* 3.2 12.8 - - - -
208P ALA* 2.8 32.0 + - - +
334P ALA 2.9 17.8 + - - -
335P ILE 3.6 3.4 - - - -
337P ARG* 1.3 73.4 - - - +
339P ALA* 1.3 62.1 + - - +
342P GLY* 2.8 30.5 + - - -
343P VAL 2.8 25.9 + - - +
345P ILE* 3.4 7.5 - - - +
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Residues in contact with ALA 339 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228O ARG* 5.6 3.6 + - - -
208P ALA 3.2 18.3 + - - +
209P TYR* 4.7 0.6 - - - +
210P THR* 3.6 41.1 + - + +
335P ILE 3.0 16.9 + - - +
336P TYR* 3.9 6.5 - - + +
338P SER* 1.3 78.6 - - - +
340P ARG* 1.3 64.6 + - - +
342P GLY* 3.9 3.8 + - - -
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Residues in contact with ARG 340 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204M GLU* 6.2 0.3 - - - -
230M ARG* 5.6 5.4 - - - +
344M ARG* 4.3 6.2 + - - -
346M PRO* 3.3 34.7 - - + +
347M LEU 3.4 21.8 - - - +
348M PRO* 2.8 42.3 + - + +
349M LEU* 3.9 1.4 - - - +
350M ASP* 3.3 43.6 + - - +
336P TYR 3.1 18.0 + - - +
337P ARG* 3.9 16.5 - - - +
339P ALA* 1.3 79.2 - - - +
341P ASP* 1.3 91.9 + - - +
342P GLY 3.8 0.2 + - - -
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Residues in contact with ASP 341 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344M ARG* 4.1 13.3 + - - +
346M PRO* 3.4 16.4 - - + +
337P ARG* 2.9 24.3 + - - +
340P ARG* 1.3 121.3 + - - +
342P GLY* 1.3 61.5 + - - +
343P VAL* 3.4 21.2 + - + +
345P ILE* 4.9 4.5 - - - +
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Residues in contact with GLY 342 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344M ARG* 5.0 3.8 - - - -
344O ARG* 4.1 25.3 + - - +
207P TYR* 3.5 27.1 + - - -
338P SER 2.8 18.6 + - - -
339P ALA 3.9 3.6 + - - -
340P ARG 3.5 2.0 - - - -
341P ASP* 1.3 72.9 - - - +
343P VAL* 1.3 58.7 + - - +
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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) + - + + + + + -
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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