Contacts of the helix formed by residues 341 - 345 (chain L) in PDB entry 2B4X
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 341 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101L GLN* 2.7 22.8 + - - +
336L GLN* 4.3 21.1 - - + +
339L GLY* 4.1 8.5 - - - +
340L LEU* 1.3 77.3 - - - +
342L ASP* 1.3 87.7 + - - +
343L LEU 3.3 1.8 - - - -
344L PHE* 2.8 19.5 + - - +
345L SER* 3.3 9.8 + - - -
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Residues in contact with ASP 342 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97L ASP* 3.2 30.6 - - - +
98L THR* 3.1 19.0 + - - +
101L GLN* 2.8 30.0 + - - +
341L VAL* 1.3 86.2 - - - +
343L LEU* 1.3 56.9 + - - +
345L SER* 2.6 31.7 + - - -
348L LYS* 3.5 34.4 - - - +
349L SER* 3.2 11.0 + - - -
350L LYS* 5.4 0.2 - - - +
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Residues in contact with LEU 343 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87L PHE* 3.5 33.4 - - + -
90L THR* 3.9 10.8 - - + -
98L THR* 3.5 29.3 - - + +
101L GLN* 5.1 0.4 + - - -
102L LEU* 4.3 7.4 - - + -
340L LEU* 4.0 22.8 - - + +
341L VAL 3.1 0.6 + - - -
342L ASP* 1.3 78.2 - - - +
344L PHE* 1.3 57.2 + - + +
349L SER* 3.4 10.9 + - - -
351L LEU* 3.9 22.7 - - + -
364L VAL* 2.7 63.0 + - + -
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Residues in contact with PHE 344 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87L PHE* 4.6 7.6 - + - -
331L LEU 4.6 0.4 - - - -
332L LYS* 3.8 41.1 - - + -
335L LEU* 3.9 24.0 - - + -
336L GLN* 3.9 19.5 - - + +
340L LEU* 3.4 46.0 - - + -
341L VAL* 2.8 12.6 + - - +
343L LEU* 1.3 75.8 - - + +
345L SER* 1.3 61.0 + - - +
346L PRO* 3.5 8.3 - - - +
363L TYR* 4.0 4.8 - - - -
364L VAL* 3.4 40.5 - - + +
365L SER 4.5 3.3 - - - +
366L ASP* 4.5 6.7 - - - -
367L ALA* 4.5 3.4 - - + -
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Residues in contact with SER 345 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341L VAL 3.3 5.6 + - - -
342L ASP* 2.6 20.8 + - - -
344L PHE* 1.3 70.8 - - - +
346L PRO* 1.3 64.7 - - - +
347L GLU* 2.8 21.0 + - - +
348L LYS* 3.0 29.0 + - - +
349L SER* 3.0 27.4 + - - -
363L TYR* 3.9 1.1 - - - -
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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