Contacts of the helix formed by residues 324 - 338 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU* 3.9 9.9 - - - -
33B GLU* 3.2 24.4 + - - +
35B PHE* 4.1 4.9 - - - +
321B ASP* 3.2 16.5 - - - +
323B THR* 1.3 82.7 + - - +
325B PRO* 1.4 72.4 - - - +
327B VAL* 3.5 0.5 + - - +
328B LEU 3.3 7.4 + - - -
354B TRP* 4.3 2.9 - - - -
355B TYR* 3.5 3.1 + - - -
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Residues in contact with PRO 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 4.8 0.7 - - + -
19B TRP* 4.6 13.9 - - + +
33B GLU* 3.3 10.3 - - - +
324B GLY* 1.4 82.2 - - - +
326B VAL* 1.3 58.3 + - - +
328B LEU* 3.5 3.2 + - + +
329B THR* 2.6 34.7 + - - -
354B TRP* 4.4 9.0 - - + -
355B TYR* 3.7 42.3 - - + -
358B LEU* 4.6 6.7 - - + -
359B VAL* 4.2 25.4 - - + -
362B LEU* 4.1 13.7 - - + -
363B PRO* 4.9 1.0 - - - +
380B LEU* 4.9 1.1 - - + -
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TRP* 4.1 10.8 - - + +
31B LEU* 3.6 38.6 - - + +
32B GLY 4.2 0.7 - - - -
33B GLU* 3.2 32.0 + - + +
89B ILE* 4.1 11.9 - - + -
325B PRO* 1.3 73.4 - - + +
327B VAL* 1.3 60.7 + - - +
329B THR* 3.3 6.5 + - - -
330B ALA* 2.9 28.6 + - - +
359B VAL* 4.8 4.9 - - + -
378B LEU* 4.0 20.8 - - + +
380B LEU* 3.8 14.4 - - + -
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Residues in contact with VAL 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLU* 2.9 31.8 + - + +
34B THR* 5.0 1.6 - - - -
35B PHE* 6.1 0.9 - - + -
89B ILE* 4.5 3.4 - - + -
293B ASP* 4.5 7.2 - - - +
294B ILE* 3.6 20.4 - - + +
295B SER* 3.6 29.8 - - - +
320B HIS 3.9 18.4 - - - +
321B ASP* 3.9 2.7 - - - +
323B THR* 3.4 24.5 - - - +
324B GLY 3.8 0.9 - - - +
325B PRO 3.4 0.2 - - - -
326B VAL* 1.3 76.5 - - - +
328B LEU* 1.3 53.7 + - - +
330B ALA* 3.4 1.0 + - - -
331B SER* 2.6 37.8 + - - -
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ASP* 3.5 30.5 + - + +
324B GLY 3.3 7.8 + - - +
325B PRO 3.6 8.7 - - - +
326B VAL 3.3 0.2 - - - -
327B VAL* 1.3 79.3 - - - +
329B THR* 1.3 54.8 + - - +
331B SER* 3.9 2.5 + - - -
332B THR* 2.7 33.8 + - - +
344B GLN* 4.1 5.2 - - - +
345B GLU 3.3 26.7 - - - +
346B SER* 4.2 7.6 - - - -
347B VAL 5.9 0.2 - - - +
351B TYR* 4.9 10.5 - - + -
355B TYR* 4.1 19.3 - - + -
363B PRO* 3.8 33.2 - - + +
370B ILE* 4.0 19.1 - - + -
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Residues in contact with THR 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B PRO 2.6 22.1 + - - -
326B VAL* 3.5 5.4 - - - -
327B VAL 3.2 0.2 - - - -
328B LEU* 1.3 75.6 - - - +
330B ALA* 1.3 59.5 + - - +
332B THR* 3.2 4.9 + - - -
333B HIS* 3.1 34.8 + - + -
363B PRO* 3.4 17.4 - - - +
372B VAL* 4.2 0.2 - - - +
373B PRO* 3.8 24.2 - - + -
378B LEU* 3.5 31.9 - - + +
380B LEU* 3.2 22.1 - - + +
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Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 4.2 13.2 - - + -
103B ILE* 5.7 0.2 - - - -
294B ILE* 4.1 14.8 - - + -
300B LEU* 3.8 23.5 - - + +
326B VAL 2.9 16.5 + - - +
327B VAL* 4.0 2.7 - - - +
329B THR* 1.3 74.1 - - - +
331B SER* 1.3 63.1 + - - +
333B HIS* 3.3 10.6 - - - +
334B LEU 3.1 16.1 + - - -
378B LEU* 3.9 20.8 - - + +
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Residues in contact with SER 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ILE* 3.3 19.0 - - - +
319B PRO* 3.8 12.3 - - - +
320B HIS 3.6 14.0 + - - -
327B VAL 2.6 24.0 + - - -
328B LEU* 4.0 2.7 - - - -
330B ALA* 1.3 76.7 - - - +
332B THR* 1.3 51.7 + - - +
334B LEU* 3.1 9.5 + - - +
335B SER* 2.7 36.7 + - - -
344B GLN* 3.1 25.9 + - - -
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Residues in contact with THR 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ILE* 4.8 1.8 - - + -
328B LEU 2.7 21.1 + - - -
329B THR* 3.2 8.1 + - - -
331B SER* 1.3 76.1 - - - +
333B HIS* 1.3 58.9 + - - +
335B SER* 3.6 2.1 - - - -
336B LEU* 2.9 37.4 + - + +
344B GLN* 3.7 18.6 - - - +
363B PRO* 4.5 2.7 - - - +
370B ILE* 3.9 18.5 - - + +
371B THR* 3.6 40.8 - - - +
372B VAL* 3.8 7.4 - - + +
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Residues in contact with HIS 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PRO* 3.9 5.4 - - + -
103B ILE* 3.5 29.4 + - + -
104B TYR* 3.1 45.2 + + - +
107B LEU* 4.1 2.9 - - - -
329B THR* 3.1 29.8 + - + -
330B ALA* 3.3 12.6 - - - +
332B THR* 1.3 75.7 - - - +
334B LEU* 1.3 60.5 + - - +
336B LEU* 3.3 1.3 + - - -
337B ASN* 3.1 20.4 + - - +
372B VAL* 3.5 25.1 - - + +
373B PRO 5.0 1.6 - - - -
375B GLY 5.1 0.2 - - - -
377B GLY 3.3 19.3 + - - -
378B LEU* 3.0 32.3 + - - -
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 3.8 16.1 - - + +
292B LEU* 4.5 9.2 - - + -
294B ILE* 4.1 22.4 - - + -
300B LEU* 4.2 11.0 - - + -
303B ALA* 3.9 33.2 - - + +
304B ARG* 4.3 9.2 - - + +
307B ALA* 4.5 11.0 - - + -
317B VAL* 4.8 4.0 - - + -
319B PRO* 3.8 24.2 - - + -
330B ALA 3.1 11.5 + - - +
331B SER* 3.1 9.4 + - - +
333B HIS* 1.3 74.6 - - - +
335B SER* 1.3 58.1 + - - +
337B ASN* 3.2 5.7 + - - +
338B ALA* 2.9 36.0 + - + +
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Residues in contact with SER 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ARG* 2.8 24.1 + - - -
115B ILE* 3.6 31.7 - - - +
319B PRO* 3.2 17.5 - - - +
331B SER 2.7 13.9 + - - -
332B THR* 3.3 6.2 + - - -
334B LEU* 1.3 73.1 - - - +
336B LEU* 1.3 59.7 + - - +
341B ALA* 3.3 14.8 - - - +
344B GLN* 2.6 30.5 + - - +
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B TYR* 4.1 18.6 - - + -
110B LYS* 4.1 8.1 - - + -
111B CYS 2.8 25.7 + - - -
112B ARG* 3.6 27.2 + - + +
113B ASP 3.8 20.9 - - - +
114B THR 4.4 1.8 - - - -
115B ILE* 4.0 28.3 - - + +
332B THR* 2.9 27.9 + - + +
333B HIS 3.6 4.7 - - - +
335B SER* 1.3 75.7 - - - +
337B ASN* 1.3 63.1 + - - +
370B ILE 4.3 2.5 - - - +
371B THR* 4.0 3.4 - - - +
372B VAL* 4.0 33.9 - - + -
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Residues in contact with ASN 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B TYR* 3.8 9.8 - - - +
107B LEU* 3.5 47.6 + - + +
108B GLY* 3.6 4.2 + - - -
109B GLY 3.0 26.0 - - - +
110B LYS* 4.3 0.4 - - - +
111B CYS* 3.1 21.0 - - - -
304B ARG* 5.8 4.6 + - - +
333B HIS 3.1 15.9 + - - +
334B LEU* 3.2 7.7 + - - +
336B LEU* 1.3 77.4 - - - +
338B ALA* 1.3 73.9 + - - +
339B PRO* 3.3 4.4 - - - +
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Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ARG* 2.7 27.4 + - - -
307B ALA* 4.3 17.0 - - + -
317B VAL* 5.7 2.2 - - + -
334B LEU* 2.9 25.9 + - + +
337B ASN* 1.3 79.2 - - - +
339B PRO* 1.3 66.4 - - + +
340B ASN* 3.8 15.9 - - - +
341B ALA* 3.1 16.7 + - + +
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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