Contacts of the helix formed by residues 348 - 354 (chain A) in PDB entry 4BN4
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 VAL 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A THR 3.5 21.1 - - - +
321A SER* 3.4 22.9 - - - +
322A LEU* 3.8 14.8 - - + +
342A LEU* 4.0 12.7 - - + +
344A ASN* 4.0 9.0 - - - +
346A ASP* 3.6 24.9 - - + +
347A LEU* 1.4 81.0 - - - +
349A GLY* 1.3 71.1 + - - +
350A PRO 3.6 0.2 - - - -
351A LEU* 3.2 18.2 + - - +
352A ALA* 3.9 4.3 - - - -
1395A AR6 4.5 2.0 - - - +
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Residues in contact with GLY 349 (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 SER 4.3 2.4 + - - -
322A LEU* 4.0 16.6 - - - -
348A VAL* 1.3 75.7 - - - +
350A PRO* 1.3 68.3 - - - +
352A ALA* 2.9 18.1 + - - +
353A TRP* 3.0 27.0 + - - +
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Residues in contact with PRO 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A LEU* 4.1 9.4 - - + -
328A ALA* 3.3 36.8 - - + +
329A SER* 5.3 0.4 - - - -
331A THR* 3.3 15.3 - - - +
332A GLU* 3.7 31.2 - - + +
340A ARG* 4.5 4.7 - - - +
349A GLY* 1.3 82.4 - - - +
351A LEU* 1.3 57.5 + - - +
352A ALA 3.2 0.2 - - - -
353A TRP* 4.9 1.6 - - + -
354A HIS* 2.7 47.5 + - + +
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Residues in contact with LEU 351 (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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317A ILE* 3.7 26.0 - - + -
322A LEU* 4.5 4.7 - - + -
331A THR* 4.1 11.7 - - + +
340A ARG* 3.9 35.9 - - + +
342A LEU* 4.3 22.4 - - + -
347A LEU* 3.8 25.2 - - + +
348A VAL 3.2 10.3 + - - +
349A GLY 3.1 1.0 - - - -
350A PRO* 1.3 79.1 - - - +
352A ALA* 1.3 58.1 + - - +
355A PRO* 4.1 14.7 - - - +
359A ASP* 3.6 33.3 - - + +
360A VAL 5.1 2.0 - - - +
361A ALA* 6.3 0.7 - - + -
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Residues in contact with ALA 352 (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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347A LEU* 3.7 41.4 - - + +
348A VAL* 3.4 6.1 + - - -
349A GLY 2.9 8.8 + - - +
351A LEU* 1.3 79.9 - - - +
353A TRP* 1.3 79.5 + - + +
354A HIS 3.7 0.4 - - - -
355A PRO* 4.0 7.9 - - - +
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Residues in contact with TRP 353 (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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349A GLY* 3.0 32.4 + - - +
350A PRO* 4.9 1.1 - - + -
352A ALA* 1.3 88.0 - - + +
354A HIS* 1.3 78.3 + - + +
355A PRO* 3.3 9.7 - - - +
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Residues in contact with HIS 354 (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 GLU* 2.9 35.8 - - - +
340A ARG* 3.2 12.6 + - - -
350A PRO* 2.7 27.5 + - + +
353A TRP* 1.3 89.2 + - + +
355A PRO* 1.3 67.5 - - - +
356A ARG* 4.0 4.9 + - - +
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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