Contacts of the helix formed by residues 331 - 342 (chain A) in PDB entry 3MBL
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 SER 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A GLU* 2.7 28.8 + - - -
330A PHE* 1.3 75.8 - - - +
332A LEU* 1.3 63.8 + - - +
333A GLU* 3.2 7.8 + - - -
334A PHE* 3.1 13.3 + - - +
335A GLN* 3.2 17.7 + - - +
363A ARG* 2.9 24.9 + - - -
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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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330A PHE 3.5 1.4 + - - -
331A SER* 1.3 72.1 - - - +
333A GLU* 1.3 64.2 + - - +
335A GLN* 3.4 22.6 + - + +
336A ASP* 3.0 29.5 + - - +
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Residues in contact with GLU 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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331A SER* 3.1 17.6 - - - +
332A LEU* 1.3 84.0 + - + +
334A PHE* 1.3 59.8 + - - +
336A ASP* 3.5 3.7 + - - +
337A PHE* 2.9 28.8 + - - +
358A HIS* 3.3 9.0 - - - -
359A ALA* 3.8 24.4 - - + +
360A PHE* 3.5 19.9 - - + +
363A ARG* 3.9 17.2 + - + +
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Residues in contact with PHE 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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163A GLU* 3.3 39.7 - - + +
166A LEU* 3.9 34.5 - - + -
253A LEU* 4.5 17.0 - - + -
257A ALA* 4.2 6.7 - - + -
325A LEU* 3.4 23.1 - - + -
330A PHE* 3.7 15.9 - + + -
331A SER* 3.1 10.2 + - - +
333A GLU* 1.3 73.9 - - - +
335A GLN* 1.3 67.6 + - - +
337A PHE* 3.0 11.8 + + - +
338A VAL* 3.0 31.3 + - + +
360A PHE* 3.4 37.1 - + + -
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Residues in contact with GLN 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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325A LEU* 4.1 30.0 - - + +
326A PRO 4.1 10.2 + - - -
327A SER* 4.1 12.7 + - - -
328A GLY 3.8 17.2 - - - +
330A PHE* 2.6 31.5 + - + +
331A SER 3.2 10.5 + - - +
332A LEU* 3.6 23.4 - - + +
334A PHE* 1.3 75.8 - - - +
336A ASP* 1.3 58.1 + - - +
338A VAL* 3.5 3.4 - - - +
339A ASN* 2.9 39.8 + - - +
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Residues in contact with ASP 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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332A LEU 3.0 17.3 + - - +
333A GLU* 3.9 4.7 - - - +
334A PHE 3.1 0.2 - - - -
335A GLN* 1.3 76.4 - - - +
337A PHE* 1.3 60.5 + - - +
339A ASN* 3.5 12.4 + - - +
340A LYS* 2.8 55.6 + - - +
358A HIS* 2.8 27.6 + - + +
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Residues in contact with PHE 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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170A SER* 4.1 8.7 - - - -
174A ILE* 3.9 14.8 - - + -
249A MET* 4.3 9.0 - - + -
253A LEU* 3.7 30.1 - - + -
333A GLU 2.9 18.7 + - - +
334A PHE* 3.4 4.5 - + - +
336A ASP* 1.3 76.6 - - - +
338A VAL* 1.3 69.0 + - + +
340A LYS* 3.0 13.8 + - - +
341A CYS* 3.0 22.6 + - - -
355A LEU* 3.8 24.2 - - + +
358A HIS* 3.5 32.5 - + + +
360A PHE* 3.7 20.6 - + + -
361A ILE* 3.6 31.6 - - + -
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Residues in contact with VAL 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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250A GLY* 4.7 4.9 - - - +
253A LEU* 4.6 11.4 - - + -
254A VAL* 4.2 22.7 - - + -
323A PRO 5.2 0.2 - - - +
324A LYS 5.1 0.4 - - - -
325A LEU* 4.2 28.0 - - + +
334A PHE* 3.0 36.6 + - + +
335A GLN 3.5 10.3 - - - +
337A PHE* 1.3 77.1 - - + +
339A ASN* 1.3 75.3 + - - +
341A CYS* 2.9 10.3 + - - +
342A LEU* 2.9 32.5 + - + +
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Residues in contact with ASN 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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323A PRO 4.8 2.4 - - - +
324A LYS* 4.4 21.4 - - - +
325A LEU 4.9 0.9 + - - -
335A GLN* 2.9 33.2 + - - +
336A ASP* 3.2 15.1 + - - +
338A VAL* 1.3 82.0 - - - +
340A LYS* 1.3 64.0 + - + +
342A LEU* 3.2 14.7 + - - -
343A ILE* 3.4 18.3 + - - +
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Residues in contact with LYS 340 (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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336A ASP* 2.8 44.1 + - - +
337A PHE* 3.0 9.8 + - - +
339A ASN* 1.3 79.1 - - - +
341A CYS* 1.3 60.1 + - - +
343A ILE* 3.6 23.3 - - + +
348A GLU 5.9 0.4 - - - +
349A ARG* 3.7 1.9 - - - +
350A ALA* 3.1 44.0 + - + +
355A LEU* 4.5 5.2 - - + -
358A HIS* 4.3 12.1 + - + +
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Residues in contact with CYS 341 (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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246A ILE* 3.8 19.3 - - - +
247A TRP* 3.6 12.6 + - - -
249A MET* 3.8 29.2 - - - -
250A GLY* 3.7 22.9 - - - -
337A PHE* 3.0 25.5 + - - -
338A VAL* 2.9 8.8 + - - +
340A LYS* 1.3 79.2 - - - +
342A LEU* 1.3 57.8 + - - +
343A ILE 3.3 1.8 - - - -
349A ARG* 2.9 22.8 - - - -
355A LEU* 3.9 13.2 - - - -
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Residues in contact with LEU 342 (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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247A TRP* 3.2 51.2 - - + +
250A GLY* 3.9 7.9 - - - -
251A LEU* 3.5 14.8 - - + +
254A VAL* 4.0 20.9 - - + -
322A PRO* 3.2 33.4 - - + +
323A PRO* 3.3 39.0 - - + +
338A VAL* 2.9 20.0 + - + +
339A ASN* 3.2 7.7 + - - +
341A CYS* 1.3 77.3 - - - +
343A ILE* 1.3 63.2 + - - +
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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