Contacts of the helix formed by residues 338 - 343 (chain A) in PDB entry 4LXZ
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 TYR 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A HIS* 3.4 25.6 - + - -
41A ARG* 3.3 31.2 + - + +
42A MET* 3.7 35.0 - - + -
45A ASN* 3.9 22.9 - - + -
336A ASN* 2.9 10.8 + - - +
337A ASP* 1.3 102.1 + - + +
339A PHE* 1.3 64.2 + - - +
340A GLU* 3.2 8.5 - - - -
341A TYR* 2.9 46.6 + + + +
342A PHE* 3.3 10.6 - - + -
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Residues in contact with PHE 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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332A GLU* 5.7 2.9 - - - -
333A LEU* 3.6 31.2 - - + -
334A PRO 3.6 17.3 - - - -
335A TYR* 3.7 33.0 - + + -
336A ASN* 3.1 25.9 + - - +
338A TYR* 1.3 75.7 - - - +
340A GLU* 1.3 66.0 + - - +
342A PHE* 3.2 16.1 + + - +
346A PHE* 3.3 56.0 - + + -
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Residues in contact with GLU 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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337A ASP 3.9 8.6 - - - +
338A TYR* 3.4 3.6 - - - -
339A PHE* 1.3 83.5 + - - +
341A TYR* 1.3 89.3 + - + +
342A PHE 3.2 0.9 + - - -
343A GLY* 3.5 9.8 + - - -
346A PHE* 4.3 8.8 - - - -
405A PG4 3.4 26.0 - - - +
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Residues in contact with TYR 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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38A HIS* 3.2 23.3 + + - -
42A MET* 3.5 39.5 - - + -
310A ILE* 3.9 17.0 - - + -
311A ARG* 3.1 31.1 - - + -
338A TYR* 2.9 35.4 + + + +
340A GLU* 1.3 102.5 - - + +
342A PHE* 1.3 58.2 + - + +
343A GLY 3.3 0.9 - - - -
405A PG4 3.4 46.7 - - - +
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Residues in contact with PHE 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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42A MET* 4.0 11.2 - - + -
46A LEU* 4.1 15.5 - - + -
311A ARG* 3.3 30.5 - - + -
314A ALA* 3.9 20.9 - - + -
315A ARG* 3.0 39.6 + - + +
333A LEU* 3.2 30.3 - - + -
336A ASN* 3.6 21.8 - - - -
338A TYR* 3.3 33.4 - - + -
339A PHE* 3.2 14.2 + - - +
341A TYR* 1.3 75.3 - - + +
343A GLY* 1.3 64.9 + - - +
345A ASP* 3.5 0.5 - - - +
346A PHE* 2.9 26.4 + - + -
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Residues in contact with GLY 343 (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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311A ARG* 4.6 3.3 + - - -
315A ARG* 5.1 0.3 + - - -
340A GLU 3.5 9.0 + - - -
341A TYR 3.3 3.7 - - - +
342A PHE* 1.3 83.9 - - - +
344A PRO* 1.3 69.4 - - - +
345A ASP* 3.3 2.5 - - - +
346A PHE* 3.5 20.2 - - - -
405A PG4 3.3 25.2 - - - +
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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