Contacts of the helix formed by residues 375 - 388 (chain B) in PDB entry 2PY5
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 GLU 375 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LYS* 4.6 14.8 - - + -
374B SER* 1.3 82.5 - - - +
376B GLY* 1.3 71.8 + - - +
377B ALA 3.3 2.3 + - - -
378B ILE* 3.6 5.5 + - - +
379B LYS* 3.5 30.8 + - - +
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Residues in contact with GLY 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASP 3.5 21.1 - - - -
137B PHE 4.4 0.4 - - - -
138B LYS* 3.8 27.1 - - - +
375B GLU* 1.3 78.2 + - - +
377B ALA* 1.3 63.8 + - - -
379B LYS* 3.2 3.0 + - - +
380B GLN* 3.0 28.6 + - - +
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Residues in contact with ALA 377 (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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137B PHE* 3.5 44.7 + - + +
179B ILE* 3.6 35.0 - - + -
375B GLU 3.3 1.2 + - - -
376B GLY* 1.3 70.5 - - - -
378B ILE* 1.3 59.8 + - + +
380B GLN* 3.1 4.9 + - - +
381B LEU* 3.0 32.4 + - - +
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Residues in contact with ILE 378 (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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179B ILE* 4.3 15.3 - - + -
183B GLN* 3.7 35.0 - - + +
367B TRP* 5.6 0.8 - - + -
370B ILE* 3.6 15.9 - - + -
374B SER* 3.6 24.9 - - - +
375B GLU 3.6 4.1 + - - +
376B GLY 3.4 0.4 - - - -
377B ALA* 1.3 73.6 - - + +
379B LYS* 1.3 60.5 + - - +
381B LEU* 3.2 8.0 + - + +
382B ALA* 2.9 28.4 + - - +
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Residues in contact with LYS 379 (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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371B LYS* 3.7 40.6 + - + +
374B SER* 3.7 21.7 + - - +
375B GLU* 3.5 37.9 + - - +
376B GLY 3.2 8.6 + - - +
378B ILE* 1.3 77.9 - - - +
380B GLN* 1.3 73.0 + - - +
382B ALA* 3.3 7.5 + - - +
383B LYS* 3.0 31.9 + - + +
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Residues in contact with GLN 380 (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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128B PHE* 5.8 5.4 - - + -
136B ASP* 3.5 36.6 + - + +
137B PHE* 3.6 31.9 - - + -
376B GLY* 3.0 25.2 + - - +
377B ALA 3.5 5.8 - - - +
379B LYS* 1.3 93.7 - - - +
381B LEU* 1.3 58.6 + - - +
383B LYS* 3.2 33.2 + - - +
384B LEU* 2.9 27.1 + - - +
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Residues in contact with LEU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 4.3 0.7 - - + -
137B PHE* 4.0 22.7 - - + -
179B ILE* 3.9 20.2 - - + -
180B GLN* 3.7 57.2 - - + +
183B GLN* 4.1 14.1 - - + -
185B LEU* 4.2 13.6 - - + +
367B TRP* 4.9 2.9 - - + -
377B ALA 3.0 19.2 + - - +
378B ILE* 3.7 7.4 - - - +
379B LYS 3.2 0.2 - - - -
380B GLN* 1.3 74.7 - - - +
382B ALA* 1.3 59.6 + - - +
384B LEU* 3.2 13.5 + - + +
385B MET* 2.9 33.4 + - - +
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Residues in contact with ALA 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B TRP* 3.5 43.7 - - + +
370B ILE* 3.8 4.0 - - + -
371B LYS* 3.6 17.9 - - - +
378B ILE 2.9 14.4 + - - +
379B LYS 3.3 7.8 + - - +
381B LEU* 1.3 73.3 - - - +
383B LYS* 1.3 64.5 + - - +
385B MET* 3.2 3.5 + - - +
386B LEU* 3.0 28.9 + - - +
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Residues in contact with LYS 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LYS* 3.9 28.7 - - + +
379B LYS* 3.0 35.1 + - + +
380B GLN* 3.2 32.5 + - - +
382B ALA* 1.3 74.9 - - - +
384B LEU* 1.3 57.7 + - - +
386B LEU* 3.2 9.1 + - - +
387B ASN* 2.9 46.5 + - - +
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Residues in contact with LEU 384 (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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125B LYS 3.4 24.5 - - - +
126B LEU* 4.9 3.4 - - + -
127B PRO* 3.7 31.6 - - + -
128B PHE* 4.5 15.5 - - + -
137B PHE* 5.8 0.9 - - + -
180B GLN* 3.9 13.9 - - - +
185B LEU* 6.3 0.9 - - + -
190B ALA* 3.9 12.8 - - + +
380B GLN 2.9 14.1 + - - +
381B LEU* 3.5 19.5 - - + +
382B ALA 3.2 0.2 - - - -
383B LYS* 1.3 76.7 - - - +
385B MET* 1.3 62.7 + - + +
387B ASN* 4.5 4.0 - - + +
388B SER* 2.7 47.2 + - - +
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Residues in contact with MET 385 (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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185B LEU* 3.7 27.6 - - + -
190B ALA 5.0 0.7 - - - +
193B ASP* 3.5 25.1 - - - +
194B SER* 2.8 41.9 + - - -
197B GLY* 4.4 6.7 - - - -
363B PHE* 3.5 24.2 - - + -
367B TRP* 3.6 54.5 - - + +
381B LEU 2.9 18.2 + - - +
382B ALA 3.5 7.9 - - - +
384B LEU* 1.3 77.1 - - + +
386B LEU* 1.3 62.0 + - - +
388B SER 3.7 1.0 + - - -
389B LEU 4.0 1.2 + - - -
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Residues in contact with LEU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B PRO* 3.9 27.3 - - + +
258B MET* 5.2 6.4 - - - +
363B PHE* 4.4 7.0 - - + +
364B ILE* 3.9 35.8 - - + +
367B TRP* 3.7 31.4 - - + +
368B THR* 3.9 20.2 - - - +
371B LYS* 4.4 16.8 - - + +
382B ALA 3.0 21.6 + - - +
383B LYS* 3.2 7.4 + - - +
385B MET* 1.3 78.2 - - - +
387B ASN* 1.3 62.8 + - - +
388B SER 3.7 0.2 + - - -
389B LEU* 4.2 8.8 + - - +
390B TYR* 5.3 0.9 + - - -
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Residues in contact with ASN 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B SER* 5.6 3.4 + - - +
254B TYR* 6.1 1.3 - - - +
255B PRO* 4.2 19.9 - - - +
383B LYS* 2.9 31.4 + - - +
384B LEU* 4.1 6.1 - - + +
386B LEU* 1.3 81.8 - - - +
388B SER* 1.3 62.6 + - - +
389B LEU 3.4 1.6 + - - -
390B TYR* 4.5 17.4 - - - -
391B GLY 5.5 0.2 + - - -
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Residues in contact with SER 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ALA* 3.7 21.6 - - - +
191B GLY* 3.5 19.0 - - - -
194B SER* 3.2 12.4 - - - -
384B LEU* 2.7 40.5 + - - +
385B MET 3.7 0.2 + - - -
386B LEU 3.4 0.6 - - - -
387B ASN* 1.3 78.9 - - - +
389B LEU* 1.3 62.1 + - - +
390B TYR 3.8 0.2 - - - -
391B GLY* 4.6 3.7 + - - -
392B LYS* 3.9 6.1 + - - +
4E C 6.0 0.9 + - - -
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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