Contacts of the helix formed by residues 276 - 280 (chain C) in PDB entry 4LXA
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 PRO 276 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A THR* 6.4 0.4 - - - -
255C GLU* 3.5 26.7 - - - +
270C TRP* 3.4 35.4 - - + +
274C THR 3.1 8.9 - - - +
275C THR* 1.3 82.8 - - + +
277C TRP* 1.3 66.0 + - - +
278C ASN* 2.9 5.4 + - - -
279C ILE* 3.1 36.6 + - + +
280C PHE* 3.8 5.6 - - + -
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Residues in contact with TRP 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C THR* 2.9 43.1 + - + -
276C PRO* 1.3 71.0 - - - +
278C ASN* 1.3 68.9 + - - +
280C PHE* 3.0 18.8 + - - +
302C PRO* 3.7 27.8 - - + +
303C GLN* 3.4 56.4 - - + +
306C LEU* 3.8 18.6 - - + -
320C TYR* 3.4 43.1 - + - -
363C ASP* 4.1 6.3 - - - +
364C GLU* 4.9 8.3 - - - +
366C ARG* 2.8 18.5 + - - +
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Residues in contact with ASN 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ALA* 2.8 33.1 + - - +
251A ALA* 4.2 16.2 - - - +
253A SER* 2.9 20.0 + - - +
254A THR 5.9 0.7 - - - +
209C ASN* 6.0 0.3 + - - -
276C PRO 2.9 2.1 + - - -
277C TRP* 1.3 86.3 - - - +
279C ILE* 1.3 63.8 + - + +
280C PHE 3.2 4.8 - - - +
363C ASP* 4.5 8.0 - - - +
364C GLU* 4.8 4.2 + - - +
365C PHE* 4.2 24.5 - - - +
366C ARG* 3.7 17.0 + - - +
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Residues in contact with ILE 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ALA 5.5 2.7 - - - +
254A THR* 4.2 26.9 - - + +
279A ILE* 5.8 1.8 - - + -
209C ASN* 6.3 0.2 - - - -
251C ALA* 3.2 31.7 - - - +
252C SER* 3.5 26.7 + - - +
254C THR* 4.6 11.2 - - + +
255C GLU* 4.0 31.2 - - + +
257C PHE* 4.5 0.4 - - + -
276C PRO* 3.1 35.0 - - + +
278C ASN* 1.3 81.6 - - + +
280C PHE* 1.3 74.4 - - + +
281C PRO* 4.0 0.9 - - - +
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Residues in contact with PHE 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C ASN* 5.1 0.4 - - - -
248C ILE* 4.4 10.3 - - + -
252C SER* 3.9 21.8 - - - -
257C PHE* 3.4 31.0 - + - -
261C PHE* 5.0 4.0 - + - -
262C TRP* 4.4 10.8 - + - -
270C TRP* 4.0 15.9 - + - -
275C THR* 5.5 0.9 - - + -
276C PRO* 3.8 14.4 - - + -
277C TRP* 3.0 9.2 + + - +
278C ASN 4.0 0.6 - - - +
279C ILE* 1.3 92.9 - - + +
281C PRO* 1.3 59.1 - - - +
302C PRO* 3.5 20.7 - - + +
305C TYR* 3.5 11.9 - + - +
306C LEU* 3.7 36.3 - - + -
322C PHE* 6.3 0.2 - + - -
366C ARG* 2.8 34.8 + - - -
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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