Contacts of the helix formed by residues 321 - 342 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126M LEU* 3.1 16.4 - - + +
128M VAL* 3.9 5.5 - - - +
317M GLU* 5.0 7.3 - - - +
318M PRO* 3.9 26.2 - - + +
319M GLU 4.1 0.8 - - - -
320M THR* 1.3 75.8 - - - +
322M GLY* 1.3 55.2 + - - +
323M ARG* 3.9 15.5 + - - +
324M GLU* 2.7 27.6 + - - +
325M GLY* 2.8 30.5 + - - -
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Residues in contact with GLY 322 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105M MET* 3.6 4.5 - - - +
116M VAL* 3.9 9.4 - - - -
126M LEU* 3.0 38.2 + - - +
128M VAL* 4.1 7.0 - - - -
321M ASP* 1.3 74.1 - - - +
323M ARG* 1.3 53.4 + - - +
325M GLY* 2.8 3.8 + - - -
326M LEU* 2.6 34.8 + - - +
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Residues in contact with ARG 323 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116M VAL* 3.6 19.9 - - + +
120M ASP* 2.9 40.6 + - - -
321M ASP* 3.4 13.8 + - - +
322M GLY* 1.3 73.1 - - - +
324M GLU* 1.3 60.3 + - - +
326M LEU* 3.2 20.9 + - + +
327M GLN* 2.8 26.1 - - - +
179P GLU* 2.7 43.2 + - - +
180P TRP* 3.7 23.9 - - - +
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Residues in contact with GLU 324 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133M ARG* 2.6 53.4 + - - +
194M ASP* 4.7 1.7 - - - +
198M TRP* 4.1 9.9 - - - +
319M GLU 3.9 3.4 - - - +
320M THR* 3.7 12.8 - - + -
321M ASP* 2.7 32.8 + - - +
323M ARG* 1.3 72.7 - - - +
325M GLY* 1.3 62.0 + - - +
327M GLN* 3.3 29.2 + - - +
328M SER* 4.0 2.3 + - - -
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Residues in contact with GLY 325 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105M MET* 3.3 19.4 - - - +
128M VAL* 4.3 17.3 - - - -
130M LYS* 5.6 3.4 - - - -
194M ASP* 6.0 0.2 - - - -
320M THR* 4.8 3.8 - - - -
321M ASP 2.8 14.5 + - - -
322M GLY 2.8 3.5 + - - -
324M GLU* 1.3 75.9 - - - +
326M LEU* 1.3 61.2 + - - +
328M SER* 3.3 11.6 + - - -
329M LEU* 3.2 16.1 + - - +
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Residues in contact with LEU 326 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105M MET* 3.3 5.5 - - + -
109M TRP* 3.4 35.7 - - + -
112M GLY* 3.9 24.5 - - - -
113M LYS* 4.0 14.1 - - + +
116M VAL* 3.8 27.4 - - + -
322M GLY 2.6 11.8 + - - +
323M ARG* 3.2 20.6 - - + +
325M GLY* 1.3 78.0 - - - +
327M GLN* 1.3 59.0 + - - +
329M LEU* 3.1 9.5 + - + +
330M ALA* 2.9 31.0 + - - +
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Residues in contact with GLN 327 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133M ARG* 5.8 1.3 - - - +
194M ASP* 5.8 0.7 - - - +
197M ASP* 3.6 39.8 + - + +
323M ARG* 2.8 26.0 + - - +
324M GLU* 3.4 22.2 - - - +
325M GLY 3.3 0.4 - - - -
326M LEU* 1.3 77.9 - - - +
328M SER* 1.3 65.3 + - - +
329M LEU 3.2 0.3 + - - -
330M ALA* 3.4 7.8 + - - +
331M LEU* 3.2 22.3 + - - +
218P GLU* 5.4 8.3 + - - -
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Residues in contact with SER 328 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M LYS* 3.9 20.1 + - - -
190M SER 4.6 3.6 - - - -
193M VAL* 3.9 5.5 - - - +
194M ASP* 3.9 38.5 + - - +
197M ASP* 5.7 1.3 - - - +
324M GLU 4.0 1.6 + - - -
325M GLY* 3.3 11.0 + - - -
326M LEU 3.4 0.4 - - - -
327M GLN* 1.3 81.5 - - - +
329M LEU* 1.3 59.9 + - - +
331M LEU* 3.5 9.1 + - - +
332M LEU* 3.0 37.6 + - - +
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Residues in contact with LEU 329 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104M PRO* 5.0 3.4 - - + -
105M MET* 4.3 7.6 - - + -
106M ALA* 3.4 36.1 - - + +
107M THR 4.8 2.9 - - - -
108M ARG 5.1 0.4 - - - -
109M TRP* 4.1 24.9 - - + -
112M GLY* 4.0 27.4 - - - -
186M MET* 4.2 17.5 - - + -
325M GLY 3.2 10.4 + - - +
326M LEU* 3.1 15.0 + - + +
327M GLN 3.0 0.8 - - - -
328M SER* 1.3 80.8 + - - +
330M ALA* 1.3 52.9 + - - +
332M LEU* 3.3 11.5 + - + +
333M THR* 2.8 42.4 + - - +
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Residues in contact with ALA 330 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109M TRP* 3.7 24.5 - - + -
326M LEU 2.9 15.5 + - - +
327M GLN* 3.6 9.6 - - - +
329M LEU* 1.3 71.9 - - - +
331M LEU* 1.3 60.6 + - + +
333M THR* 3.1 2.4 + - - -
334M ALA* 2.8 30.7 + - - +
347M LEU* 4.4 9.9 - - + -
348M PRO* 6.3 0.4 - - + -
349M LEU* 3.6 20.3 - - + +
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Residues in contact with LEU 331 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193M VAL* 3.8 28.0 - - + +
196M LEU* 4.1 14.6 - - + -
197M ASP* 4.5 13.2 - - + +
203M VAL* 3.6 25.6 - - + -
206M VAL* 3.6 29.6 - - + -
227M LEU* 4.9 3.1 - - + -
327M GLN 3.2 9.4 + - - +
328M SER* 3.6 9.4 - - - +
330M ALA* 1.3 78.0 - - - +
332M LEU* 1.3 57.4 + - - +
334M ALA* 3.2 5.0 + - + +
335M ILE* 2.8 38.4 + - + +
347M LEU* 4.0 20.6 - - + +
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Residues in contact with LEU 332 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104M PRO* 4.6 9.2 - - + -
185M PHE* 3.5 42.0 - - + +
186M MET* 3.7 32.1 - - + +
190M SER* 4.1 20.4 - - - -
193M VAL* 3.9 21.1 - - + -
328M SER* 3.0 30.8 + - - +
329M LEU* 3.3 8.9 + - + +
331M LEU* 1.3 76.0 - - - +
333M THR* 1.3 62.0 + - - +
335M ILE* 3.4 6.5 + - + +
336M TYR* 3.0 31.4 + - + +
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Residues in contact with THR 333 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107M THR 5.5 1.0 + - - -
109M TRP* 3.5 35.9 + - + +
186M MET* 5.5 3.8 - - - +
329M LEU* 2.8 28.2 + - - +
330M ALA 3.1 5.1 + - - -
332M LEU* 1.3 76.8 - - - +
334M ALA* 1.3 54.4 + - - +
336M TYR* 3.2 5.8 + - - +
337M ARG* 2.8 64.7 + - + +
349M LEU* 3.9 9.2 - - + -
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Residues in contact with ALA 334 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206M VAL* 3.9 15.5 - - + -
330M ALA 2.8 16.1 + - - +
331M LEU* 3.6 6.7 - - + +
333M THR* 1.3 77.6 - - - +
335M ILE* 1.3 56.7 + - - +
337M ARG* 4.6 0.7 - - - -
338M SER* 2.9 32.6 + - - -
345M ILE* 3.6 31.1 - - + +
347M LEU* 3.9 18.8 - - + -
349M LEU* 4.4 2.9 - - + -
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Residues in contact with ILE 335 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185M PHE* 4.2 35.0 - - + -
193M VAL* 4.3 17.5 - - + -
196M LEU* 5.9 1.6 - - + -
206M VAL* 4.2 15.9 - - + -
208M ALA* 3.7 16.9 - - + +
210M THR* 4.6 4.3 - - + -
225M ALA* 3.9 24.5 - - + -
227M LEU* 5.7 2.0 - - + -
237M ILE* 4.9 2.9 - - + -
331M LEU* 2.8 28.9 + - + +
332M LEU* 3.7 6.7 - - + +
334M ALA* 1.3 76.9 - - - +
336M TYR* 1.3 66.6 + - + +
338M SER* 3.6 1.4 - - - -
339M ALA* 2.7 33.1 + - - +
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Residues in contact with TYR 336 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107M THR 5.7 0.7 - - - -
178M TRP* 3.8 26.5 - + + -
182M GLY* 4.4 0.4 - - - -
183M GLY 3.0 17.9 + - - -
185M PHE* 3.9 14.1 - + + -
186M MET* 3.2 44.9 + - + -
210M THR* 5.0 5.8 - - + -
220M GLU* 2.3 46.0 + - - -
332M LEU* 3.0 21.5 + - + +
333M THR* 3.8 5.6 - - + +
335M ILE* 1.3 83.4 - - + +
337M ARG* 1.3 64.2 + - + +
339M ALA* 3.4 5.2 + - + +
340M ARG* 3.0 24.3 + - - +
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Residues in contact with ARG 337 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350K ASP* 5.1 13.4 + - - +
109M TRP* 4.1 18.8 - - - +
110M GLU* 6.2 1.0 - - - +
333M THR* 2.8 46.0 + - + +
334M ALA* 3.9 3.1 - - - +
336M TYR* 1.3 71.1 - - + +
338M SER* 1.3 54.5 + - - +
340M ARG* 3.1 17.9 + - - +
341M ASP* 2.7 49.0 + - - +
345M ILE* 3.9 24.5 - - + +
349M LEU* 3.8 25.0 - - - +
350M ASP 5.4 3.8 + - - +
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Residues in contact with SER 338 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206M VAL* 4.4 2.5 - - - -
207M TYR* 3.3 12.5 - - - -
208M ALA* 2.8 34.4 + - - +
334M ALA 2.9 18.4 + - - -
335M ILE* 3.6 3.4 - - - -
337M ARG* 1.3 76.4 - - - +
339M ALA* 1.3 65.9 + - - +
341M ASP 4.5 0.2 - - - +
342M GLY* 3.0 21.7 + - - -
343M VAL 2.8 27.6 + - - +
345M ILE* 3.5 8.2 - - - +
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Residues in contact with ALA 339 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208M ALA 3.4 14.0 + - - +
209M TYR* 4.7 1.2 - - - +
210M THR* 3.4 44.0 + - + +
335M ILE 2.7 20.9 + - - +
336M TYR* 3.8 8.1 - - + +
338M SER* 1.3 74.3 - - - +
340M ARG* 1.3 63.4 + - - +
342M GLY* 4.2 3.3 + - - -
228N ARG* 5.8 1.9 + - - -
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Residues in contact with ARG 340 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344K ARG* 4.5 5.5 + - - -
346K PRO* 3.4 36.5 - - + +
347K LEU 3.6 17.0 - - - +
348K PRO* 2.9 43.4 + - + +
349K LEU* 3.8 4.2 + - - +
350K ASP* 3.2 41.6 + - - +
336M TYR 3.0 18.5 + - - +
337M ARG* 3.8 15.3 - - - +
339M ALA* 1.3 81.0 - - - +
341M ASP* 1.3 90.0 + - - +
342M GLY 3.8 0.2 + - - -
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Residues in contact with ASP 341 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344K ARG* 3.9 13.6 + - - +
346K PRO* 3.5 15.5 - - - +
337M ARG* 2.7 30.1 + - - +
340M ARG* 1.3 113.8 + - - +
342M GLY* 1.3 62.2 + - - +
343M VAL* 4.1 21.6 - - + +
345M ILE* 5.1 2.3 - - + +
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Residues in contact with GLY 342 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344K ARG* 5.1 3.6 - - - -
207M TYR* 3.5 23.9 + - - -
338M SER 3.0 11.8 + - - -
339M ALA 4.9 2.0 - - - -
340M ARG 3.5 2.4 - - - -
341M ASP* 1.3 78.2 - - - +
343M VAL* 1.3 64.8 + - - +
344N ARG* 3.1 28.3 + - - +
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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