Contacts of the helix formed by residues 325 - 334 (chain A) in PDB entry 2NYM
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 GLN 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A VAL* 4.0 20.3 - - + +
285A PRO* 5.9 1.6 - - - +
288A GLN* 3.2 37.4 + - - +
321A VAL* 2.8 34.0 + - + +
324A SER* 1.3 97.4 + - - +
326A ILE* 1.3 73.4 + - + +
328A PRO* 3.1 14.9 - - - +
329A CYS* 4.1 2.3 - - - -
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Residues in contact with ILE 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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284A VAL* 4.4 13.0 - - + +
287A PHE* 4.5 10.3 - - + -
288A GLN* 5.9 0.4 - - + -
291A MSE 4.4 25.1 - - + -
306A VAL* 4.9 6.7 - - + -
309A PHE* 4.6 15.5 - - + -
310A CYS* 4.6 15.7 - - - -
313A LEU* 4.9 1.6 - - + -
321A VAL* 3.0 30.9 + - + +
322A ILE* 3.9 12.1 - - + +
325A GLN* 1.3 79.8 - - + +
327A LEU* 1.3 65.9 + - - +
328A PRO* 2.9 7.5 - - - -
329A CYS* 3.1 14.9 + - - +
330A ILE* 3.2 33.1 + - + -
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Residues in contact with LEU 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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322A ILE* 2.8 23.6 + - + +
323A MSE 3.5 40.2 - - - +
326A ILE* 1.3 71.9 - - - +
328A PRO* 1.3 64.4 - - - +
330A ILE* 3.9 18.8 - - + -
331A LYS* 3.2 38.5 + - + +
356A LEU* 4.9 2.5 - - + -
364A HIS* 3.9 26.7 - - + +
365A LEU* 3.7 27.1 - - + -
368A LEU* 4.7 2.2 - - + -
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Residues in contact with PRO 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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288A GLN* 5.7 1.6 - - - +
292A LYS* 5.3 1.3 - - - +
323A MSE 4.0 7.0 - - - +
324A SER* 3.6 20.0 - - - +
325A GLN 3.1 15.9 - - - +
326A ILE 2.9 7.9 - - - +
327A LEU* 1.3 96.3 - - + +
329A CYS* 1.3 64.9 + - - +
331A LYS* 3.3 21.2 + - + +
332A GLU* 3.4 9.5 + - - +
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Residues in contact with CYS 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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288A GLN* 3.7 37.5 - - - -
291A MSE 4.2 23.8 - - + -
292A LYS* 3.3 41.7 - - + +
325A GLN 4.1 5.2 - - - -
326A ILE 3.1 5.7 + - - +
328A PRO* 1.3 80.2 - - - +
330A ILE* 1.3 66.6 + - - +
332A GLU* 2.9 13.7 + - - +
333A LEU* 2.9 19.5 + - + +
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Residues in contact with ILE 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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291A MSE 5.2 2.2 - - - -
306A VAL* 4.2 18.2 - - + -
322A ILE* 5.6 1.1 - - + +
326A ILE* 3.2 33.6 + - + +
327A LEU* 3.8 18.8 - - + +
329A CYS* 1.3 74.9 - - - +
331A LYS* 1.3 65.8 - - - +
333A LEU* 2.8 22.0 + - + +
334A VAL* 2.9 14.6 + - + +
345A LEU* 4.1 9.6 - - + -
349A ILE* 3.9 27.6 - - + -
352A LEU* 3.3 31.9 - - + -
365A LEU* 5.5 0.2 - - + -
368A LEU* 4.0 12.1 - - + -
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Residues in contact with LYS 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 LEU* 3.2 38.5 + - + +
328A PRO* 3.3 11.6 + - + +
330A ILE* 1.3 79.7 - - - +
332A GLU* 1.3 60.3 + - - +
334A VAL* 3.8 20.2 - - - +
335A SER* 4.0 7.6 + - - -
364A HIS* 3.8 32.2 + - - +
368A LEU* 4.3 17.8 - - + +
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Residues in contact with GLU 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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292A LYS* 4.4 16.2 - - - +
328A PRO 3.4 6.5 + - - +
329A CYS* 2.9 15.5 + - - +
331A LYS* 1.3 78.6 - - - +
333A LEU* 1.3 69.6 + - + +
335A SER* 3.0 28.1 + - - +
336A ASP* 3.6 1.2 + - - -
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Residues in contact with LEU 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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291A MSE 3.2 53.8 - - + +
299A ARG* 4.4 8.7 - - + -
303A SER* 3.9 20.0 - - - +
306A VAL* 5.5 1.6 - - + -
329A CYS* 2.9 17.4 + - + +
330A ILE* 2.8 9.0 + - - +
332A GLU* 1.3 79.1 - - + +
334A VAL* 1.3 63.2 + - - +
336A ASP* 2.7 28.9 + - - +
341A VAL* 4.4 21.3 - - + +
342A LYS* 4.1 7.2 - - - +
345A LEU* 3.7 22.4 - - + -
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Residues in contact with VAL 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 ILE* 2.9 23.3 + - + +
331A LYS* 3.8 9.6 - - - +
332A GLU 3.2 0.4 - - - -
333A LEU* 1.3 74.8 - - - +
335A SER* 1.3 59.6 + - - +
336A ASP 3.7 1.7 + - - -
342A LYS* 3.8 19.1 - - - +
345A LEU* 4.5 11.1 - - + +
349A ILE* 4.5 6.7 - - + -
368A LEU* 3.8 35.0 - - + +
371A ALA* 3.7 30.1 - - + -
372A GLN* 4.0 20.9 - - + +
375A ASP* 4.9 2.1 - - - +
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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