Contacts of the helix formed by residues 311 - 323 (chain D) in PDB entry 2POZ
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 SER 311 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU* 5.1 0.4 - - - -
15D SER* 6.1 1.1 - - - -
20D PRO* 4.0 20.8 - - - +
22D LEU* 3.6 4.5 - - - +
36D GLU* 2.6 32.1 + - - -
310D GLY* 1.3 78.4 - - - +
312D SER* 1.3 62.8 + - - +
313D LEU* 3.0 16.0 + - - +
314D ILE* 3.5 12.6 - - - +
315D GLU* 3.7 5.0 + - - +
338D LYS* 6.4 0.9 - - - -
343D TYR* 5.3 8.1 - - - -
344D VAL 5.3 2.2 - - - -
346D VAL* 3.4 25.3 - - - +
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Residues in contact with SER 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D SER* 1.3 74.2 - - - +
313D LEU* 1.3 61.3 + - - +
315D GLU* 3.6 10.7 + - - +
316D THR* 2.8 30.1 + - - -
338D LYS* 4.0 8.3 + - - +
343D TYR* 3.0 16.6 + - - -
345D GLU* 2.7 32.4 + - - -
346D VAL* 3.9 2.3 - - - +
347D LEU* 3.3 15.7 - - - -
350D PRO* 3.6 12.9 - - - +
351D PRO* 4.2 4.6 - - - +
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Residues in contact with LEU 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU* 3.7 22.4 - - + -
23D VAL 5.2 0.2 - - - +
34D ALA* 3.9 21.1 - - + -
35D GLY* 3.8 30.1 - - - +
36D GLU* 3.4 4.9 - - + +
98D GLN* 5.2 1.3 - - - +
311D SER* 3.0 13.4 + - - +
312D SER* 1.3 75.7 - - - +
314D ILE* 1.3 68.9 + - - +
316D THR* 3.1 3.3 + - - -
317D ALA* 2.9 21.1 + - + +
346D VAL* 3.8 9.3 - - + +
347D LEU* 3.7 10.6 - - + +
366D LEU* 4.5 15.0 - - + -
368D ALA* 4.1 23.1 - - + -
370D LEU* 4.3 9.0 - - + -
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Residues in contact with ILE 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D GLU* 2.9 46.8 + - + +
38D GLY* 4.3 11.0 - - - -
98D GLN* 4.7 1.3 - - - +
280D ASP* 3.4 28.3 - - - +
281D ILE* 4.0 15.3 - - + -
282D GLY* 3.8 15.3 - - - -
308D VAL* 5.0 4.0 - - + -
309D CYS 4.5 10.5 - - - +
310D GLY* 3.9 16.2 - - - +
311D SER 3.5 12.1 - - - +
313D LEU* 1.3 73.0 - - - +
315D GLU* 1.3 64.4 + - + +
317D ALA* 3.5 6.8 + - - +
318D THR* 2.8 34.3 + - - +
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Residues in contact with GLU 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D VAL* 4.8 10.1 - - + -
310D GLY 5.9 0.2 - - - +
311D SER 3.7 7.5 + - - +
312D SER* 3.6 10.7 + - - +
313D LEU 3.1 0.8 - - - -
314D ILE* 1.3 85.9 - - + +
316D THR* 1.3 62.3 + - - +
318D THR* 3.2 14.6 + - - -
319D LEU* 3.2 15.7 + - + +
331D HIS* 3.1 29.9 + - + +
332D GLU 3.9 3.7 - - - +
333D HIS* 2.6 36.8 + - - -
338D LYS* 4.8 7.4 + - - -
351D PRO* 3.4 26.0 - - + +
358D PHE* 4.2 3.3 - - - -
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Residues in contact with THR 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D SER 2.8 23.1 + - - -
313D LEU 3.6 3.6 - - - -
315D GLU* 1.3 72.7 - - - +
317D ALA* 1.3 66.5 + - - +
319D LEU* 3.0 27.5 + - + +
320D GLN* 3.4 7.6 + - - +
347D LEU* 3.2 15.3 - - + +
349D ASN 5.2 1.4 + - - +
351D PRO* 3.4 15.1 - - + +
361D PRO* 4.2 15.3 - - + +
366D LEU 3.6 20.6 - - - +
367D GLY 3.8 13.9 - - - +
368D ALA* 4.2 7.9 - - + -
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Residues in contact with ALA 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D GLN* 4.1 15.0 - - + +
281D ILE* 3.6 19.1 - - + -
287D LEU* 3.4 14.2 - - + +
313D LEU* 2.9 16.4 + - + +
314D ILE 3.8 1.3 - - - +
316D THR* 1.3 78.1 - - - +
318D THR* 1.3 60.8 + - - +
320D GLN* 3.2 26.8 - - - +
366D LEU* 4.3 26.6 - - + +
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Residues in contact with THR 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D ILE* 3.7 20.6 - - + +
306D PRO* 4.0 13.0 - - + -
308D VAL* 2.9 33.1 - - + +
314D ILE* 2.8 19.5 + - - +
315D GLU 3.3 10.5 - - - -
316D THR 3.1 0.2 - - - -
317D ALA* 1.3 74.9 - - - +
319D LEU* 1.3 60.0 + - - +
320D GLN 3.1 0.7 - - - -
321D LEU* 3.1 8.0 + - + +
322D GLU* 3.0 49.2 + - + +
331D HIS* 4.2 3.6 - - + -
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Residues in contact with LEU 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D VAL* 4.3 14.6 - - + -
315D GLU* 3.3 13.9 - - + +
316D THR* 3.0 14.5 + - + +
318D THR* 1.3 74.2 - - - +
320D GLN* 1.3 65.3 + - - +
322D GLU* 3.2 20.9 - - - +
323D ALA* 3.0 27.0 + - - +
331D HIS* 3.8 16.2 - - + +
351D PRO* 4.0 26.2 - - + -
358D PHE* 4.4 12.1 - - + -
359D GLU 4.2 9.0 - - - +
360D MSE 3.8 9.5 - - + +
361D PRO* 3.7 29.5 - - + +
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Residues in contact with GLN 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D PRO* 3.7 2.7 - - - +
112D VAL* 2.9 32.3 + - + +
113D TYR* 3.2 47.4 + - - +
116D PHE* 5.1 3.0 - - + -
287D LEU* 4.5 11.9 - - + -
316D THR 4.0 6.3 - - - +
317D ALA* 3.2 16.4 + - - +
318D THR 3.1 0.2 - - - -
319D LEU* 1.3 80.4 - - - +
321D LEU* 1.3 61.4 + - - +
323D ALA 3.7 2.3 + - - -
324D ASN* 3.8 3.6 + - - +
361D PRO* 3.2 33.3 + - - +
363D GLY 5.1 0.4 + - - -
365D GLY 3.7 9.3 + - - -
366D LEU* 3.4 31.3 + - + +
367D GLY* 4.6 0.6 - - - +
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Residues in contact with LEU 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D PHE* 5.1 6.7 - - + -
281D ILE* 3.9 11.7 - - + -
287D LEU* 3.9 37.7 - - + +
290D THR* 3.4 26.7 - - + -
291D LYS* 3.9 17.5 - - + +
294D CYS* 4.5 6.1 - - - -
306D PRO* 4.1 24.9 - - + -
317D ALA 3.7 1.2 + - - -
318D THR* 3.1 8.9 + - + +
320D GLN* 1.3 76.7 - - - +
322D GLU* 1.3 59.0 + - - +
323D ALA 3.1 2.2 - - - -
324D ASN* 2.9 21.5 + - - +
325D ILE* 3.1 35.4 + - + +
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Residues in contact with GLU 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ARG* 2.6 38.6 + - - -
124D VAL* 4.1 10.5 - - + +
306D PRO* 4.0 16.8 - - + +
318D THR* 3.0 25.3 + - + +
319D LEU* 3.2 21.9 + - - +
321D LEU* 1.3 74.4 - - + +
323D ALA* 1.3 51.2 + - - +
324D ASN 3.2 0.2 - - - -
325D ILE* 4.3 5.2 - - - -
328D PHE* 3.2 40.0 - - + +
330D ILE 4.0 1.2 - - - +
331D HIS* 2.6 43.3 + - - +
332D GLU 4.8 0.2 + - - -
360D MSE 5.3 0.2 - - - -
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Residues in contact with ALA 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D TYR* 3.9 21.5 - - + -
119D LYS* 3.3 6.7 - - + +
120D ILE* 2.9 28.4 + - - +
121D ARG* 3.8 10.5 + - - +
319D LEU 3.0 18.0 + - - +
320D GLN 3.9 6.3 - - - +
321D LEU 3.1 0.2 + - - -
322D GLU* 1.3 78.8 - - - +
324D ASN* 1.3 59.4 + - - +
360D MSE 3.4 28.2 - - + -
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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
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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