Contacts of the helix formed by residues 311 - 325 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LEU* 5.4 0.2 - - - -
15A SER* 6.1 0.7 - - - -
20A PRO* 4.2 16.9 - - - +
22A LEU* 3.8 3.7 - - - +
36A GLU* 2.5 34.7 + - - -
310A GLY* 1.3 77.1 - - - -
312A SER* 1.3 66.3 + - - +
313A LEU* 3.1 8.7 + - - +
314A ILE* 3.4 2.8 + - - +
315A GLU* 3.4 21.6 + - - +
338A LYS* 4.6 2.5 - - - +
343A TYR* 5.7 4.3 - - - -
344A VAL 5.1 4.7 - - - -
346A VAL* 3.4 27.2 - - - +
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Residues in contact with SER 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A SER* 1.3 75.1 - - - +
313A LEU* 1.3 61.9 + - - +
315A GLU* 3.4 12.3 + - - +
316A THR* 2.9 30.7 + - - -
338A LYS* 3.5 8.3 + - - +
343A TYR* 3.3 14.8 + - - -
345A GLU* 2.7 30.8 + - - -
346A VAL* 4.0 2.8 - - - +
347A LEU* 3.6 16.6 - - - -
350A PRO* 3.8 10.5 - - - +
351A PRO* 4.3 4.4 - - - +
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Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 4.3 9.2 - - + -
34A ALA* 3.9 19.5 - - + -
35A GLY* 3.6 38.8 - - - +
36A GLU* 3.4 14.1 - - + +
98A GLN* 5.3 1.6 - - - +
311A SER* 3.0 6.1 + - - +
312A SER* 1.3 78.9 - - - +
314A ILE* 1.3 59.1 + - - +
316A THR* 3.1 3.6 + - - -
317A ALA* 2.9 26.0 + - + +
346A VAL* 3.7 11.9 - - + +
347A LEU* 4.0 11.0 - - + -
366A LEU* 4.4 16.8 - - + -
368A ALA* 3.9 23.8 - - + -
370A LEU* 4.2 11.2 - - + -
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Residues in contact with ILE 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLU* 3.0 47.6 + - + +
38A GLY* 4.3 11.0 - - - -
98A GLN* 4.8 2.2 - - - +
280A ASP* 3.5 25.4 - - - +
281A ILE* 4.0 14.1 - - + -
282A GLY* 3.6 20.2 - - - +
308A VAL* 5.1 4.0 - - + -
309A CYS 4.6 7.2 - - - +
310A GLY* 3.8 17.0 - - - +
311A SER 3.4 11.9 - - - +
313A LEU* 1.3 74.1 - - - +
315A GLU* 1.3 62.8 + - + +
317A ALA* 3.8 5.3 - - - +
318A THR* 2.8 36.8 + - - +
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Residues in contact with GLU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A VAL* 5.0 17.0 - - + +
310A GLY 3.9 9.7 + - - +
311A SER 3.4 15.8 + - - +
312A SER* 3.7 9.9 - - - +
313A LEU 3.1 0.6 - - - -
314A ILE* 1.3 82.8 - - + +
316A THR* 1.3 62.4 + - - +
318A THR* 3.3 8.5 + - - -
319A LEU* 3.2 26.1 + - - +
331A HIS* 4.3 9.1 + - + +
332A GLU 5.8 0.4 - - - -
333A HIS* 3.1 33.4 + - - -
338A LYS* 3.2 30.4 + - - -
351A PRO* 4.8 10.7 - - + +
358A PHE* 4.2 7.2 - - + -
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Residues in contact with THR 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A SER 2.9 18.8 + - - -
313A LEU 3.6 3.4 - - - -
315A GLU* 1.3 75.1 - - - +
317A ALA* 1.3 64.2 + - - +
319A LEU* 3.1 25.4 + - + +
320A GLN* 3.5 6.9 + - - +
347A LEU* 3.3 10.1 - - + +
349A ASN 5.2 1.1 + - - +
351A PRO* 3.2 24.3 - - + +
361A PRO* 4.2 15.3 - - + +
366A LEU 3.3 21.8 - - - +
367A GLY 4.1 7.9 - - - +
368A ALA* 4.0 13.7 - - + -
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Residues in contact with ALA 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLN* 4.3 11.7 - - + +
281A ILE* 3.5 19.3 - - + -
287A LEU* 3.5 10.9 - - + +
313A LEU* 2.9 15.8 + - + +
314A ILE* 3.8 5.6 - - - +
316A THR* 1.3 76.3 - - - +
318A THR* 1.3 62.8 + - - +
320A GLN* 3.0 22.4 + - - +
366A LEU* 4.1 33.8 - - + +
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Residues in contact with THR 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ILE* 3.5 24.9 - - + +
306A PRO* 4.0 10.3 - - + -
308A VAL* 2.9 33.7 - - + +
314A ILE 2.8 21.2 + - - -
315A GLU* 3.5 6.5 - - - -
316A THR 3.2 0.4 - - - -
317A ALA* 1.3 76.6 - - - +
319A LEU* 1.3 62.1 + - - +
321A LEU* 3.1 13.9 + - + +
322A GLU* 3.1 37.1 + - + +
331A HIS* 4.3 3.8 - - + -
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A VAL* 4.1 16.4 - - + -
315A GLU 3.2 11.8 + - - +
316A THR* 3.1 13.7 + - + +
318A THR* 1.3 74.6 - - - +
320A GLN* 1.3 66.6 + - - +
322A GLU* 3.5 21.7 - - - +
323A ALA* 3.0 26.5 + - - +
331A HIS* 3.7 15.7 - - + +
351A PRO* 4.1 24.5 - - + -
358A PHE* 4.1 12.8 - - + -
359A GLU 3.8 13.5 - - - +
360A MSE 3.9 8.2 - - + +
361A PRO* 3.8 29.6 - - + -
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Residues in contact with GLN 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A PRO* 3.7 3.5 - - - +
112A VAL* 2.9 32.3 + - + -
113A TYR* 2.9 49.8 + - - +
116A PHE* 5.0 3.5 - - + -
287A LEU* 4.5 8.1 - - + -
316A THR 3.5 5.1 + - - +
317A ALA 3.0 16.6 + - - +
319A LEU* 1.3 79.5 - - - +
321A LEU* 1.3 59.1 + - - +
323A ALA 3.7 2.8 + - - -
324A ASN* 3.8 3.8 + - - +
361A PRO* 3.6 22.2 + - - +
363A GLY 4.9 0.4 + - - -
365A GLY 3.5 13.4 + - - -
366A LEU* 3.2 41.2 + - + -
367A GLY* 4.7 1.0 - - - -
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PHE* 5.1 7.2 - - + -
281A ILE* 4.0 11.7 - - + -
287A LEU* 3.8 24.6 - - + +
290A THR* 3.6 22.9 - - + -
291A LYS* 3.7 38.8 - - + +
294A CYS* 4.5 6.5 - - - -
306A PRO* 4.2 26.2 - - + -
317A ALA 3.7 0.8 + - - -
318A THR 3.1 8.8 + - - +
320A GLN* 1.3 76.7 - - - +
322A GLU* 1.3 57.9 + - - +
323A ALA 3.1 4.7 - - - -
324A ASN* 2.9 21.0 + - - +
325A ILE* 3.0 29.3 + - + +
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Residues in contact with GLU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ARG* 2.6 38.2 + - - -
124A VAL* 4.0 10.2 - - + +
306A PRO* 3.4 28.2 - - + +
318A THR* 3.1 22.2 + - + +
319A LEU* 3.4 15.5 + - + +
321A LEU* 1.3 76.1 - - + +
323A ALA* 1.3 54.1 + - - +
324A ASN 3.2 0.2 - - - -
325A ILE* 4.2 8.5 - - - -
328A PHE* 3.3 35.7 - - + -
331A HIS* 2.5 42.3 + - - +
360A MSE 4.7 0.2 - - - -
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Residues in contact with ALA 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A TYR* 3.7 28.7 - - + -
119A LYS* 3.5 5.5 - - + -
120A ILE* 2.8 30.0 + - - +
121A ARG* 3.7 11.6 + - - +
319A LEU 3.0 17.2 + - - +
320A GLN 3.8 1.1 - - - +
321A LEU 3.1 0.6 - - - -
322A GLU* 1.3 78.7 - - - +
324A ASN* 1.3 59.6 + - - +
360A MSE 3.6 26.4 - - + -
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Residues in contact with ASN 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A TYR* 3.6 7.3 + - + -
116A PHE* 3.1 39.9 + - + +
118A GLY 2.7 26.1 + - - +
120A ILE* 3.2 16.4 - - - +
291A LYS* 2.6 33.3 + - - +
320A GLN 3.9 10.5 - - - +
321A LEU* 2.9 9.0 + - - +
323A ALA* 1.3 82.1 - - - +
325A ILE* 1.3 66.2 + - - +
326A THR 3.6 0.5 + - - -
69E GLU* 3.5 17.0 - - - +
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Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ILE* 3.8 1.0 - - - +
121A ARG* 2.8 32.4 + - - -
291A LYS* 4.7 10.8 - - + +
294A CYS* 3.9 34.5 - - + -
304A VAL* 4.2 11.9 - - + -
306A PRO* 4.9 1.1 - - + -
321A LEU* 3.0 42.0 + - + +
322A GLU* 4.2 4.7 - - - -
324A ASN* 1.3 81.2 - - - +
326A THR* 1.3 59.0 + - - +
327A ASN* 4.0 7.6 - - - +
328A PHE* 3.7 39.0 + - + +
69E GLU* 5.5 0.2 - - - -
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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