Contacts of the helix formed by residues 325 - 339 (chain A) in PDB entry 2PID
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 PRO 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ARG* 3.8 5.6 - - - +
323A PHE 3.3 6.3 - - - +
324A LEU* 1.3 88.3 - - + +
326A LEU* 1.3 66.3 + - + +
327A PRO* 4.1 11.4 - - + -
328A GLU* 2.9 37.3 + - + +
329A ILE* 3.1 9.7 + - - +
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Residues in contact with LEU 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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41A ALA* 5.2 9.6 - - + +
44A ALA* 4.3 23.1 - - + -
45A ARG* 3.9 36.3 - - + +
319A LYS* 4.5 17.9 - - - +
324A LEU 3.6 0.6 + - - -
325A PRO* 1.3 70.6 - - + +
327A PRO* 1.3 73.4 - - + +
329A ILE* 3.0 14.4 + - + +
330A ASP* 2.9 30.6 + - - +
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Residues in contact with PRO 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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325A PRO* 3.5 10.1 - - + -
326A LEU* 1.3 96.9 - - + +
328A GLU* 1.3 59.2 - - - +
330A ASP* 3.2 15.1 - - + +
331A HIS* 3.2 19.2 + - - +
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Residues in contact with GLU 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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324A LEU* 4.3 9.1 - - + +
325A PRO* 2.9 34.4 + - + +
327A PRO* 1.3 77.4 - - - +
329A ILE* 1.3 65.7 + - - +
331A HIS* 3.2 12.6 + - + +
332A ILE* 3.0 31.5 + - + +
348A ARG* 2.8 40.6 + - - +
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Residues in contact with ILE 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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45A ARG* 4.1 2.5 - - - +
315A GLU* 4.0 29.6 - - + +
318A LEU* 3.8 40.8 - - + +
319A LYS* 3.8 27.4 - - + +
324A LEU* 3.6 32.3 - - + +
325A PRO 3.1 7.3 + - - +
326A LEU* 3.0 13.1 + - - +
328A GLU* 1.3 73.1 - - - +
330A ASP* 1.3 68.8 + - - +
332A ILE* 3.2 8.6 + - - +
333A MET* 2.9 26.6 + - + +
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Residues in contact with ASP 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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315A GLU* 5.4 5.2 - - - +
326A LEU* 2.9 25.4 + - - +
327A PRO* 3.2 18.5 - - + +
329A ILE* 1.3 78.9 - - - +
331A HIS* 1.3 57.7 + - - +
333A MET* 3.1 7.3 + - - +
334A GLN* 2.8 40.2 + - - +
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Residues in contact with HIS 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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327A PRO 3.2 10.0 + - - +
328A GLU* 3.2 18.1 + - + +
329A ILE 3.2 0.4 - - - -
330A ASP* 1.3 80.2 - - - +
332A ILE* 1.3 64.9 + - + +
334A GLN* 3.2 23.0 + - + +
335A LEU* 2.8 61.0 + - + +
338A LYS* 5.8 3.8 - - - -
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Residues in contact with ILE 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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318A LEU* 4.3 10.3 - - + -
324A LEU* 3.9 11.9 - - + -
328A GLU* 3.0 22.7 + - + +
329A ILE* 3.2 10.3 + - - +
331A HIS* 1.3 82.6 - - + +
333A MET* 1.3 59.3 + - - +
335A LEU* 3.7 8.1 - - + +
336A HIS* 3.1 24.8 + - - +
344A GLY* 4.3 4.3 - - - -
345A PRO* 3.6 36.3 - - + +
348A ARG* 3.5 45.5 - - + +
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Residues in contact with MET 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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311A ASP* 4.7 5.6 - - + +
314A VAL* 3.5 25.8 - - + -
315A GLU* 3.0 45.1 - - + +
318A LEU* 4.2 10.1 - - - -
329A ILE* 2.9 20.0 + - + +
330A ASP* 3.6 5.4 - - - +
332A ILE* 1.3 75.4 - - - +
334A GLN* 1.3 65.7 + - - +
336A HIS* 2.9 25.2 + - - +
337A VAL* 3.2 11.5 + - - +
345A PRO* 3.8 25.8 - - + -
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Residues in contact with GLN 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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330A ASP* 2.8 32.5 + - - +
331A HIS* 3.2 34.5 + - + +
333A MET* 1.3 72.7 - - - +
335A LEU* 1.3 61.2 + - - +
336A HIS 3.2 0.9 + - - -
337A VAL* 3.3 18.9 + - - +
338A LYS* 3.3 22.9 + - + +
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Residues in contact with LEU 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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331A HIS* 2.8 43.5 + - + +
332A ILE* 3.7 7.6 - - + +
334A GLN* 1.3 78.7 - - - +
336A HIS* 1.3 56.1 + - - +
338A LYS* 3.3 24.5 + - - +
339A GLU* 3.0 59.6 + - + +
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Residues in contact with HIS 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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311A ASP* 2.8 36.7 - - - +
314A VAL* 5.5 0.4 - - + -
332A ILE 3.1 13.6 + - - +
333A MET* 2.9 23.7 + - + +
335A LEU* 1.3 75.2 - - - +
337A VAL* 1.3 65.4 + - + +
338A LYS 3.0 1.3 - - - -
339A GLU* 2.9 16.9 + - - +
340A PRO* 2.9 46.8 + - + +
343A ARG* 3.7 9.5 + - - -
344A GLY 4.2 3.8 - - - -
345A PRO* 3.3 37.1 - - + +
346A GLN* 4.3 1.3 - - - -
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Residues in contact with VAL 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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333A MET 3.2 11.6 + - - +
334A GLN* 3.3 12.3 + - - +
336A HIS* 1.3 79.5 + - + +
338A LYS* 1.3 65.2 + - + +
340A PRO* 3.4 14.7 - - - +
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Residues in contact with LYS 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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331A HIS* 5.8 3.8 - - - -
334A GLN* 3.3 23.4 - - + +
335A LEU* 3.3 24.9 + - - +
336A HIS 3.0 0.4 - - - -
337A VAL* 1.3 82.6 - - + +
339A GLU* 1.3 65.3 + - + +
340A PRO* 3.7 3.5 - - - +
341A GLU* 4.4 2.4 - - - +
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Residues in contact with GLU 339 (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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335A LEU* 3.0 42.9 + - + +
336A HIS* 2.9 13.4 + - - -
338A LYS* 1.3 86.9 - - + +
340A PRO* 1.3 68.0 - - - +
341A GLU* 2.9 15.1 + - - +
342A ARG* 2.8 61.7 + - + +
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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
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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