Contacts of the helix formed by residues 325 - 334 (chain A) in PDB entry 1B3U
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 ILE 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A VAL* 4.7 7.9 - - + +
286A PHE* 4.6 11.2 - - + -
287A GLN* 5.2 5.6 - - + -
290A MET* 4.6 17.3 - - + -
305A VAL* 5.0 2.5 - - + -
308A PHE* 4.6 13.7 - - + -
309A CYS* 4.0 23.8 - - - -
312A LEU* 5.3 0.2 - - + -
320A VAL* 3.1 21.7 + - + +
321A ILE* 3.7 13.2 - - + +
324A GLN* 1.3 89.0 - - + +
326A LEU* 1.3 67.8 + - - +
327A PRO 3.2 2.2 - - - -
328A CYS* 2.9 17.4 + - - +
329A ILE* 2.9 38.2 + - + -
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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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321A ILE* 2.7 23.8 + - + +
322A MET* 3.2 39.7 - - + +
325A ILE* 1.3 72.3 - - - +
327A PRO* 1.3 71.4 - - + +
329A ILE* 3.0 15.8 + - + +
330A LYS* 2.9 35.7 + - + +
351A LEU* 6.3 0.2 - - + -
355A LEU* 5.4 4.0 - - + -
363A HIS* 3.6 22.2 - - + +
364A LEU* 4.4 15.0 - - + -
367A LEU* 4.1 24.7 - - + -
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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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322A MET 3.5 13.5 - - - +
323A SER 3.9 14.1 - - - +
324A GLN 3.8 11.2 - - - +
325A ILE 3.4 3.8 - - - -
326A LEU* 1.3 95.6 - - + +
328A CYS* 1.3 62.6 + - - +
330A LYS* 3.3 23.4 + - + +
331A GLU* 3.4 20.5 + - - +
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Residues in contact with CYS 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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287A GLN* 4.1 15.5 - - - -
290A MET* 3.5 32.3 - - + -
291A LYS* 3.2 39.0 + - - +
324A GLN 3.5 17.0 - - - -
325A ILE 2.9 7.2 + - - +
327A PRO* 1.3 78.2 - - - +
329A ILE* 1.3 65.8 + - - +
331A GLU* 3.2 5.6 + - - +
332A LEU* 3.2 25.9 + - - +
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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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290A MET* 4.7 4.3 - - - -
305A VAL* 3.5 35.4 - - + -
321A ILE* 6.3 1.1 - - + -
325A ILE* 2.9 38.8 + - + +
326A LEU* 3.0 15.2 + - + +
328A CYS* 1.3 76.3 - - - +
330A LYS* 1.3 62.9 + - - +
332A LEU* 3.2 9.7 + - + +
333A VAL* 3.2 20.4 + - - +
344A LEU* 4.1 8.5 - - + +
348A ILE* 3.7 29.6 - - + -
351A LEU* 3.9 16.2 - - + -
364A LEU* 6.0 0.2 - - + -
367A LEU* 4.1 11.2 - - + -
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Residues in contact with LYS 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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326A LEU* 2.9 39.4 + - + +
327A PRO* 3.4 15.3 - - + +
328A CYS 3.2 0.2 - - - -
329A ILE* 1.3 77.0 - - - +
331A GLU* 1.3 63.5 + - + +
333A VAL* 3.3 22.4 + - - +
334A SER* 3.9 6.6 + - - -
363A HIS* 4.8 14.7 + - - +
367A LEU* 4.0 28.1 - - + +
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Residues in contact with GLU 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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291A LYS* 2.7 33.8 + - - +
327A PRO 3.8 12.9 - - - +
328A CYS* 3.2 5.8 + - - +
329A ILE 3.2 0.4 - - - -
330A LYS* 1.3 78.3 - - + +
332A LEU* 1.3 63.6 + - + +
334A SER* 3.0 19.2 + - - -
335A ASP* 3.4 7.4 + - - -
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Residues in contact with LEU 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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290A MET* 3.5 54.7 - - + +
298A ARG* 4.7 4.3 - - + -
302A SER* 4.0 18.6 - - - +
305A VAL* 5.1 0.7 - - + -
328A CYS 3.2 16.9 + - - +
329A ILE* 3.2 13.2 + - + +
331A GLU* 1.3 73.8 - - + +
333A VAL* 1.3 65.2 + - - +
335A ASP* 2.9 29.2 + - - +
340A VAL* 4.1 24.5 - - + +
341A LYS* 3.9 6.8 - - - +
344A LEU* 3.9 21.0 - - + +
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Residues in contact with VAL 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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329A ILE 3.2 15.6 + - - +
330A LYS 3.5 9.4 - - - +
331A GLU 3.2 0.4 - - - -
332A LEU* 1.3 77.5 - - - +
334A SER* 1.3 60.3 + - - +
341A LYS* 3.5 18.9 - - - +
344A LEU* 3.9 16.6 - - + -
348A ILE* 4.6 3.8 - - + -
367A LEU* 4.2 28.5 - - + +
370A ALA* 3.9 24.0 - - + -
371A GLN* 3.8 30.2 + - + +
374A ASP* 5.1 1.4 - - - +
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Residues in contact with SER 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 LYS 4.3 5.6 + - - -
331A GLU* 3.0 13.6 + - - -
332A LEU 3.0 0.8 - - - -
333A VAL* 1.3 80.9 - - - +
335A ASP* 1.3 65.7 + - - +
336A ALA* 3.4 2.3 + - - -
341A LYS* 4.7 0.7 - - - -
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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