Contacts of the helix formed by residues 321 - 342 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125K ARG* 6.3 0.2 - - + -
126K LEU 3.1 14.1 - - - +
128K VAL* 4.2 3.1 - - - +
318K PRO* 3.9 28.8 - - + +
319K GLU 3.7 3.6 - - - -
320K THR* 1.3 80.6 - - - +
322K GLY* 1.3 65.1 + - - +
323K ARG* 3.8 17.0 + - - +
324K GLU* 3.0 24.9 + - - +
325K GLY* 3.1 15.4 + - - -
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Residues in contact with GLY 322 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105K MET* 3.7 6.0 - - - +
116K VAL* 4.1 11.4 - - - -
126K LEU* 2.9 40.7 + - - +
128K VAL* 4.1 6.1 - - - -
321K ASP* 1.3 74.6 - - - +
323K ARG* 1.3 54.7 + - - +
325K GLY* 2.7 23.7 + - - -
326K LEU* 3.0 9.4 + - - +
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Residues in contact with ARG 323 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116K VAL* 3.4 22.5 - - + +
120K ASP* 3.0 39.8 + - - -
321K ASP* 3.4 15.5 + - - +
322K GLY* 1.3 73.9 - - - +
324K GLU* 1.3 64.7 + - - +
326K LEU* 3.0 27.3 + - + +
327K GLN* 3.3 15.0 + - - +
179M GLU* 2.7 44.0 + - - +
180M TRP* 3.8 23.0 - - - +
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Residues in contact with GLU 324 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130K LYS* 6.0 0.2 - - - -
133K ARG* 3.0 34.2 + - - +
194K ASP* 5.1 0.5 - - - +
197K ASP* 5.1 4.5 - - - +
198K TRP* 4.3 8.7 - - - +
319K GLU 3.5 19.7 - - - +
320K THR* 3.6 16.4 - - + -
321K ASP* 3.0 23.4 + - - +
323K ARG* 1.3 76.0 - - - +
325K GLY* 1.3 63.5 + - - +
327K GLN* 3.3 36.9 + - - +
328K SER* 3.9 4.0 + - - -
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Residues in contact with GLY 325 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105K MET* 3.3 19.5 - - - +
128K VAL* 4.3 17.7 - - - -
130K LYS* 5.7 2.5 - - - -
320K THR* 4.1 4.0 - - - +
321K ASP 3.1 8.8 + - - -
322K GLY 2.7 10.5 + - - -
324K GLU* 1.3 80.1 - - - +
326K LEU* 1.3 53.5 + - - -
328K SER* 3.4 9.7 + - - -
329K LEU* 3.1 21.1 + - - +
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Residues in contact with LEU 326 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105K MET* 3.9 9.6 - - - -
109K TRP* 3.5 25.9 - - + -
112K GLY* 3.7 33.0 - - - +
113K LYS* 3.9 13.2 - - + +
116K VAL* 3.8 29.6 - - + -
322K GLY 3.0 5.7 + - - +
323K ARG* 3.0 21.0 + - + +
325K GLY* 1.3 74.9 - - - +
327K GLN* 1.3 61.3 + - - +
329K LEU* 3.6 4.5 - - + -
330K ALA* 2.7 35.7 + - - +
179M GLU* 6.2 0.2 - - - +
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Residues in contact with GLN 327 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133K ARG* 5.9 2.5 - - - +
194K ASP* 6.1 0.2 - - - +
197K ASP* 3.3 39.6 - - + +
323K ARG 3.3 9.0 + - - +
324K GLU* 3.3 29.3 + - - +
326K LEU* 1.3 83.0 + - - +
328K SER* 1.3 60.8 + - - +
330K ALA* 3.4 7.9 + - - +
331K LEU* 3.3 22.0 + - - +
218M GLU* 4.3 14.7 + - - +
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Residues in contact with SER 328 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130K LYS* 3.6 21.1 + - - -
190K SER* 5.3 1.1 - - - -
193K VAL* 4.4 8.7 - - - +
194K ASP* 4.0 33.1 + - - -
197K ASP* 6.0 3.4 - - - -
324K GLU 3.9 2.6 + - - -
325K GLY 3.4 9.4 + - - -
326K LEU 3.4 0.2 - - - -
327K GLN* 1.3 77.1 - - - +
329K LEU* 1.3 68.5 + - - +
331K LEU* 3.9 8.8 - - - +
332K LEU* 3.0 31.8 + - - +
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Residues in contact with LEU 329 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104K PRO* 5.2 2.5 - - + -
105K MET* 4.2 13.9 - - + +
106K ALA* 3.4 28.3 - - + +
107K THR 4.6 4.5 - - - -
108K ARG 4.2 2.5 - - - +
109K TRP* 3.9 26.9 - - + +
112K GLY* 3.8 28.7 - - - -
186K MET* 4.6 15.3 - - + -
325K GLY 3.1 18.3 + - - +
326K LEU* 3.3 8.9 + - + +
328K SER* 1.3 78.8 + - - +
330K ALA* 1.3 62.4 + - - +
332K LEU* 3.2 9.3 + - + -
333K THR* 2.9 32.6 + - - +
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Residues in contact with ALA 330 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109K TRP* 3.6 25.0 - - + -
326K LEU 2.7 21.9 + - - +
327K GLN* 3.6 10.3 - - - +
328K SER 3.2 0.2 - - - -
329K LEU* 1.3 71.2 - - - +
331K LEU* 1.3 58.8 + - - +
333K THR* 3.0 5.2 + - - -
334K ALA* 2.9 27.4 + - - +
347K LEU* 4.2 17.7 - - + -
348K PRO* 6.2 0.7 - - + -
349K LEU* 3.7 10.7 - - + +
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Residues in contact with LEU 331 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193K VAL* 4.0 30.5 - - + +
196K LEU* 4.2 16.8 - - + -
197K ASP* 4.9 9.6 - - + +
203K VAL* 3.9 32.1 - - + -
206K VAL* 4.0 16.6 - - + -
227K LEU* 4.8 0.9 - - + -
327K GLN 3.3 11.4 + - - +
328K SER* 3.9 8.3 - - - +
329K LEU 3.3 0.2 - - - -
330K ALA* 1.3 76.0 - - - +
332K LEU* 1.3 60.4 + - - +
334K ALA* 3.4 4.1 + - + +
335K ILE* 2.9 36.2 + - + +
347K LEU* 3.4 29.1 - - + +
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Residues in contact with LEU 332 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104K PRO* 4.7 10.1 - - + -
185K PHE* 3.6 36.3 - - + +
186K MET* 3.7 41.1 - - + +
190K SER* 4.2 14.6 - - - -
193K VAL* 4.1 21.3 - - + -
328K SER* 3.0 28.0 + - - +
329K LEU* 3.7 9.0 - - + +
331K LEU* 1.3 77.8 - - - +
333K THR* 1.3 58.2 + - - +
335K ILE* 3.5 6.3 + - + +
336K TYR* 3.0 33.6 + - + +
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Residues in contact with THR 333 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350J ASP* 6.0 0.4 - - - +
109K TRP* 3.5 28.3 + - + +
186K MET* 5.8 2.2 - - - +
329K LEU* 2.9 19.7 + - - +
330K ALA 3.4 6.5 - - - -
332K LEU* 1.3 75.7 - - - +
334K ALA* 1.3 57.4 + - - +
336K TYR* 3.2 5.7 + - + +
337K ARG* 2.6 74.2 + - + +
349K LEU* 3.9 7.9 - - + -
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Residues in contact with ALA 334 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206K VAL* 3.8 16.2 - - + -
330K ALA 2.9 13.1 + - - +
331K LEU* 3.7 8.7 - - + +
333K THR* 1.3 75.4 - - - +
335K ILE* 1.3 57.3 + - - +
337K ARG* 4.5 0.7 - - - -
338K SER* 2.8 33.1 + - - -
345K ILE* 3.6 32.7 - - + +
347K LEU* 4.2 19.1 - - + -
349K LEU* 4.5 3.7 - - + +
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Residues in contact with ILE 335 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185K PHE* 4.2 35.4 - - + -
193K VAL* 4.6 12.3 - - + -
196K LEU* 5.5 0.4 - - + -
206K VAL* 4.1 18.2 - - + -
208K ALA* 3.5 17.0 - - + +
210K THR* 4.8 4.9 - - + -
225K ALA* 3.8 24.9 - - + -
227K LEU* 5.3 3.1 - - + -
237K ILE* 4.9 4.7 - - + -
331K LEU* 2.9 31.3 + - + +
332K LEU* 3.7 8.3 - - + +
334K ALA* 1.3 77.4 - - - +
336K TYR* 1.3 70.3 + - + +
338K SER* 3.3 1.9 + - - -
339K ALA* 3.0 25.5 + - - +
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Residues in contact with TYR 336 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107K THR 5.6 0.9 - - - -
178K TRP* 4.0 26.0 - + + -
182K GLY* 4.6 0.9 - - - -
183K GLY 3.0 18.5 + - - -
185K PHE* 3.9 13.5 - + + -
186K MET* 3.2 46.4 + - + +
210K THR* 5.3 5.4 - - + -
220K GLU* 2.8 40.3 + - - -
332K LEU* 3.0 20.9 + - + +
333K THR* 3.7 6.7 - - + +
335K ILE* 1.3 79.6 - - + +
337K ARG* 1.3 66.5 + - + +
339K ALA* 3.9 4.1 - - + +
340K ARG* 2.9 25.3 + - - +
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Residues in contact with ARG 337 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350J ASP* 4.8 18.3 + - - +
109K TRP* 4.0 21.4 - - - +
110K GLU* 5.5 3.0 + - - +
333K THR* 2.6 47.4 + - + +
334K ALA* 3.8 3.4 - - - +
336K TYR* 1.3 73.6 - - - +
338K SER* 1.3 57.8 + - - +
340K ARG* 3.3 22.5 + - - +
341K ASP* 2.9 40.2 + - - +
345K ILE* 3.9 26.8 - - + +
349K LEU* 3.9 24.8 - - - +
350K ASP 5.0 5.3 + - - +
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Residues in contact with SER 338 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206K VAL* 4.5 1.6 - - - -
207K TYR* 3.3 12.6 - - - -
208K ALA* 2.9 31.2 + - - +
334K ALA 2.8 19.1 + - - -
335K ILE* 3.5 4.9 - - - -
337K ARG* 1.3 75.3 - - - +
339K ALA* 1.3 59.2 - - - +
341K ASP* 5.1 0.2 - - - -
342K GLY* 2.7 33.3 + - - -
343K VAL 2.9 27.1 + - - +
345K ILE* 3.6 9.4 - - - +
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Residues in contact with ALA 339 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208K ALA 3.2 15.8 + - - +
209K TYR* 4.7 0.7 - - - +
210K THR* 3.6 46.1 + - + +
335K ILE 3.0 16.7 + - - +
336K TYR* 3.9 6.3 - - + +
338K SER* 1.3 77.7 - - - +
340K ARG* 1.3 64.8 + - - +
342K GLY* 4.0 3.6 + - - -
228L ARG* 5.7 3.1 + - - -
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Residues in contact with ARG 340 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344J ARG* 4.0 7.3 + - - -
346J PRO* 3.3 34.3 - - + +
347J LEU 3.7 17.0 - - - +
348J PRO* 3.0 36.0 + - + +
349J LEU* 4.0 1.3 - - - -
350J ASP* 3.1 44.8 + - - +
336K TYR 2.9 17.9 + - - +
337K ARG* 3.8 17.7 - - - +
339K ALA* 1.3 81.9 - - - +
341K ASP* 1.3 90.3 + - - +
342K GLY 3.8 0.2 + - - -
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Residues in contact with ASP 341 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344J ARG* 3.8 15.8 + - - +
346J PRO* 3.3 17.8 - - - +
337K ARG* 2.9 23.5 + - - +
340K ARG* 1.3 114.4 + - - +
342K GLY* 1.3 64.1 + - - +
343K VAL* 3.8 22.1 - - + +
345K ILE* 5.0 4.2 - - + +
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Residues in contact with GLY 342 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344J ARG* 5.0 4.5 - - - -
207K TYR* 3.3 27.1 + - - -
208K ALA 5.7 0.2 - - - -
338K SER 2.7 17.7 + - - -
339K ALA 4.0 3.2 + - - -
340K ARG 3.5 2.4 + - - -
341K ASP* 1.3 74.4 - - - +
343K VAL* 1.3 59.8 + - - +
344L ARG* 4.2 18.0 + - - +
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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