Contacts of the helix formed by residues 324 - 338 (chain A) in PDB entry 2POD
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 GLY 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A LEU* 4.0 8.3 - - - -
33A GLU* 3.2 22.0 + - - +
35A PHE* 4.1 6.5 - - - -
321A ASP* 3.4 9.7 - - - +
323A THR* 1.3 82.2 + - - +
325A PRO* 1.4 75.5 - - - +
327A VAL 3.8 0.2 + - - -
328A LEU 3.5 5.0 + - - -
354A TRP* 4.1 4.3 - - - -
355A TYR* 3.2 12.4 + - - -
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Residues in contact with PRO 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.7 3.4 - - + -
19A TRP* 4.8 3.6 - - + +
33A GLU* 3.4 9.2 - - - +
324A GLY* 1.4 81.4 - - - +
326A VAL* 1.3 58.2 + - + +
328A LEU* 3.4 4.4 + - + +
329A THR* 2.8 32.2 + - - -
354A TRP* 4.5 9.0 - - + -
355A TYR* 3.5 37.9 - - + -
358A LEU* 4.4 14.1 - - + -
359A VAL* 3.9 38.6 - - + -
362A LEU* 4.1 5.4 - - + -
363A PRO* 4.8 1.6 - - - +
380A LEU* 4.8 0.7 - - - -
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Residues in contact with VAL 326 (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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19A TRP* 4.1 11.7 - - + +
31A LEU* 3.8 35.2 - - + +
32A GLY 4.4 0.7 - - - -
33A GLU* 3.2 32.8 + - + +
89A ILE* 4.1 12.8 - - + -
325A PRO* 1.3 77.7 - - + +
327A VAL* 1.3 61.6 + - - +
329A THR* 3.2 7.3 + - - -
330A ALA* 2.9 27.7 + - - +
359A VAL* 4.7 3.1 - - + -
378A LEU* 3.8 23.6 - - + -
380A LEU* 4.1 9.9 - - + -
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Residues in contact with VAL 327 (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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33A GLU* 2.9 33.3 + - + +
34A THR* 4.9 1.6 - - - -
89A ILE* 4.5 2.5 - - + -
293A ASP* 4.1 9.6 - - - +
294A ILE* 3.5 19.8 - - + +
295A SER* 3.6 29.6 - - - +
320A HIS 3.8 18.8 - - - +
321A ASP* 4.4 2.0 - - - +
323A THR* 3.4 24.7 - - - +
324A GLY 4.1 0.4 - - - +
326A VAL* 1.3 75.5 - - - +
328A LEU* 1.3 53.5 + - - +
330A ALA* 4.5 0.4 - - - -
331A SER* 2.7 38.5 + - - -
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Residues in contact with LEU 328 (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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321A ASP* 3.4 27.7 + - + +
324A GLY 3.5 6.8 + - - +
325A PRO 3.4 8.7 + - - +
326A VAL 3.3 0.6 - - - -
327A VAL* 1.3 77.9 - - - +
329A THR* 1.3 53.7 + - - +
331A SER* 3.8 1.8 - - - -
332A THR* 2.7 37.3 + - - +
344A GLN* 4.1 4.7 - - - +
345A GLU 3.4 26.5 - - - +
346A SER* 4.3 2.5 - - - -
347A VAL 5.9 0.2 - - - +
351A TYR* 4.6 17.0 - - + -
355A TYR* 3.6 26.2 - - + -
363A PRO* 4.0 25.1 - - + -
370A ILE* 4.0 19.1 - - + -
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Residues in contact with THR 329 (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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325A PRO 2.8 19.3 + - - -
326A VAL* 3.2 7.8 + - - -
328A LEU* 1.3 75.4 - - - +
330A ALA* 1.3 59.5 + - - +
332A THR* 3.3 5.0 + - - -
333A HIS* 3.0 35.2 + - + -
363A PRO* 3.3 18.0 - - - +
372A VAL* 4.2 0.5 - - - +
373A PRO* 3.8 22.0 - - + -
378A LEU* 3.4 32.3 - - + +
380A LEU* 3.3 23.4 - - + +
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Residues in contact with ALA 330 (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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89A ILE* 4.2 13.5 - - + -
103A ILE* 5.8 0.4 - - - -
294A ILE* 3.9 18.6 - - + -
300A LEU* 3.7 21.8 - - + +
326A VAL 2.9 16.5 + - - +
327A VAL* 4.5 0.2 - - - -
329A THR* 1.3 74.5 - - - +
331A SER* 1.3 65.0 + - - +
333A HIS* 3.3 10.2 + - - +
334A LEU 3.1 16.8 + - - -
378A LEU* 4.0 19.3 - - + +
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Residues in contact with SER 331 (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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294A ILE* 3.3 19.6 - - - +
319A PRO* 3.8 13.5 - - - +
320A HIS 3.4 15.6 + - - -
327A VAL 2.7 25.0 + - - -
328A LEU* 3.8 2.2 - - - -
330A ALA* 1.3 72.3 - - - +
332A THR* 1.3 55.2 + - - +
334A LEU* 3.1 8.8 + - - +
335A SER* 2.7 37.4 + - - -
344A GLN* 3.2 26.2 - - - +
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Residues in contact with THR 332 (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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115A ILE* 3.8 18.4 - - + -
328A LEU* 2.7 22.9 + - - +
329A THR* 3.3 8.0 + - - -
331A SER* 1.3 74.0 - - - +
333A HIS* 1.3 59.9 + - - +
335A SER* 3.3 4.2 + - - -
336A LEU* 2.9 30.5 + - + +
344A GLN* 3.6 18.0 + - - +
363A PRO* 4.5 2.0 - - - +
370A ILE* 3.9 12.3 - - + +
371A THR* 3.6 36.8 - - - +
372A VAL* 3.7 8.1 - - + +
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Residues in contact with HIS 333 (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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102A PRO* 3.9 6.1 - - + -
103A ILE* 3.5 27.4 - - + -
104A TYR* 3.1 43.5 + + - +
107A LEU* 4.0 2.2 - - - -
329A THR* 3.0 32.0 + - + -
330A ALA* 3.4 11.9 - - - +
331A SER 3.3 0.4 - - - -
332A THR* 1.3 74.4 - - - +
334A LEU* 1.3 61.1 + - - +
336A LEU 3.3 1.7 + - - -
337A ASN* 3.1 19.4 + - - +
372A VAL* 3.5 26.4 - - + +
373A PRO 4.9 1.8 - - - -
375A GLY 5.1 0.2 - - - -
377A GLY 3.3 20.5 + - - -
378A LEU* 3.0 30.2 + - - -
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Residues in contact with LEU 334 (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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107A LEU* 3.8 16.5 - - + +
292A LEU* 3.9 30.1 - - + -
294A ILE* 3.9 14.8 - - + -
300A LEU* 4.1 10.3 - - + -
303A ALA* 3.9 27.6 - - + +
304A ARG* 4.2 9.4 - - + +
307A ALA* 4.5 11.0 - - + -
317A VAL* 5.2 3.4 - - + -
319A PRO* 4.1 15.9 - - + -
330A ALA 3.1 13.1 + - - +
331A SER* 3.1 6.3 + - - +
333A HIS* 1.3 74.8 - - - +
335A SER* 1.3 57.2 + - - +
337A ASN* 3.2 5.7 + - - +
338A ALA* 2.9 35.9 + - + +
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Residues in contact with SER 335 (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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112A ARG* 2.7 34.4 + - - -
115A ILE* 3.6 29.3 - - - +
319A PRO* 3.1 21.0 - - - +
331A SER 2.7 13.4 + - - -
332A THR* 3.3 2.0 + - - -
334A LEU* 1.3 72.2 - - - +
336A LEU* 1.3 52.0 - - - +
341A ALA* 3.4 16.2 - - - +
343A VAL 4.3 0.7 + - - -
344A GLN* 2.9 27.1 + - - +
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Residues in contact with LEU 336 (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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104A TYR* 4.0 19.1 - - + -
110A LYS* 3.4 8.0 - - + -
111A CYS 2.9 25.1 + - - -
112A ARG* 3.6 28.0 + - + +
113A ASP 3.5 22.9 - - - +
114A THR* 4.1 1.6 - - - -
115A ILE* 3.7 26.9 - - + -
332A THR* 2.9 20.2 + - + +
333A HIS 3.6 4.7 - - - +
334A LEU 3.2 0.2 - - - -
335A SER* 1.3 76.9 - - - +
337A ASN* 1.3 60.9 + - - +
370A ILE 4.6 0.7 - - - +
371A THR* 3.8 18.2 - - - +
372A VAL* 3.9 26.5 - - + -
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Residues in contact with ASN 337 (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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104A TYR* 3.9 5.1 - - - +
107A LEU* 3.3 51.6 + - + +
108A GLY 3.6 3.8 + - - -
109A GLY 3.0 25.9 - - - +
110A LYS* 4.4 0.4 - - - +
111A CYS* 3.2 20.6 - - - -
304A ARG* 5.7 4.2 + - - +
333A HIS 3.1 15.7 + - - +
334A LEU* 3.7 10.2 + - - +
336A LEU* 1.3 77.2 - - - +
338A ALA* 1.3 71.9 + - - +
339A PRO* 3.2 5.2 - - - +
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Residues in contact with ALA 338 (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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112A ARG* 2.6 28.8 + - - +
307A ALA* 4.2 17.9 - - + -
317A VAL* 5.7 2.9 - - + -
334A LEU* 2.9 24.5 + - + +
336A LEU 3.7 0.2 - - - -
337A ASN* 1.3 78.1 - - - +
339A PRO* 1.3 62.7 - - + +
340A ASN* 3.7 15.7 - - - +
341A ALA* 3.1 19.9 + - + +
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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