Contacts of the helix formed by residues 302 - 311 (chain L) in PDB entry 4XLR
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 302 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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814I GLU* 4.1 18.4 + - - -
300L GLU 3.9 0.6 + - - -
301L PRO* 1.3 73.7 - - - +
303L TYR* 1.3 70.3 + - - +
304L GLU* 3.2 7.7 + - - +
305L GLU* 2.7 33.1 + - - +
306L ILE* 3.0 13.4 - - - +
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Residues in contact with TYR 303 (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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808I ARG* 3.1 43.1 + - - -
814I GLU* 3.1 28.7 + - - -
815I LEU 3.6 10.2 + - - -
817I PRO* 3.9 19.2 - - - +
301L PRO 3.9 0.8 + - - -
302L SER* 1.3 76.9 + - - +
304L GLU* 1.3 57.7 + - - +
306L ILE* 3.1 8.6 - - + +
307L ALA* 3.0 31.5 + - - +
316L ALA* 3.5 30.3 - - + -
319L VAL* 3.8 19.0 - - + +
320L GLU* 4.0 14.4 - - + -
323L LEU* 3.9 22.7 - - + +
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Residues in contact with GLU 304 (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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302L SER* 3.1 6.2 + - - +
303L TYR* 1.3 80.3 - - - +
305L GLU* 1.3 58.4 + - - +
307L ALA* 3.9 1.9 - - - +
308L GLU* 2.9 30.3 + - + +
315L ASP* 5.8 3.2 - - + +
316L ALA* 4.0 20.4 - - + +
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Residues in contact with GLU 305 (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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293L LEU* 4.4 3.6 - - + +
297L LEU* 3.3 24.4 - - - +
299L ARG* 5.2 3.5 + - - -
300L GLU 4.7 1.2 - - - +
301L PRO* 3.5 14.1 - - + +
302L SER* 2.7 46.5 + - - +
304L GLU* 1.3 76.7 - - - +
306L ILE* 1.3 61.6 + - - +
308L GLU* 3.6 7.4 - - - +
309L ALA* 2.9 26.3 + - - +
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Residues in contact with ILE 306 (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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286L LEU* 4.6 6.3 - - + +
289L THR* 3.6 17.5 - - + -
290L ALA* 3.5 42.4 - - + +
293L LEU* 3.6 16.8 - - + -
301L PRO* 3.9 18.6 - - + +
302L SER 3.0 18.4 - - - +
303L TYR* 3.1 21.3 - - + +
305L GLU* 1.3 78.9 - - - +
307L ALA* 1.3 61.1 + - + +
309L ALA* 2.9 19.1 + - - +
310L MET* 3.0 15.0 + - + +
319L VAL* 5.0 13.7 - - + -
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Residues in contact with ALA 307 (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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286L LEU* 5.8 0.2 - - - -
303L TYR 3.0 19.3 + - - +
304L GLU 4.0 2.7 - - - +
306L ILE* 1.3 78.6 - - - +
308L GLU* 1.3 60.3 + - - +
310L MET* 3.1 15.0 - - - +
311L GLY 3.6 0.9 + - - +
314L TRP* 3.1 29.8 - - + +
315L ASP* 3.2 39.7 - - - +
316L ALA 3.8 0.9 - - - +
319L VAL* 3.7 10.3 - - + -
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Residues in contact with GLU 308 (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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304L GLU* 2.9 21.7 + - + +
305L GLU* 3.6 8.1 - - - +
306L ILE 3.1 0.2 - - - -
307L ALA* 1.3 72.5 - - - +
309L ALA* 1.3 65.6 + - - +
310L MET 3.0 2.4 + - - -
311L GLY* 3.2 20.9 + - - +
314L TRP 4.1 4.7 + - - -
130N ARG* 4.8 5.4 + - - -
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Residues in contact with ALA 309 (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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289L THR* 4.2 14.0 - - + +
293L LEU* 3.5 25.1 - - + -
305L GLU 2.9 14.8 + - - +
306L ILE 2.9 12.2 + - - +
308L GLU* 1.3 76.9 - - - +
310L MET* 1.3 61.6 + - - +
127N GLN* 5.9 0.7 + - - -
130N ARG* 4.7 7.2 + - - +
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Residues in contact with MET 310 (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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285L LYS* 3.3 37.2 - - + +
286L LEU* 3.6 31.9 - - + -
289L THR* 3.1 31.4 - - + -
306L ILE* 3.0 17.7 + - + +
307L ALA* 3.1 14.6 - - - +
308L GLU 3.0 1.0 - - - -
309L ALA* 1.3 80.0 - - - +
311L GLY* 1.3 57.9 + - - +
314L TRP* 3.6 36.7 + - + +
123N ASP* 4.9 4.9 - - - +
126N ARG* 4.6 10.6 + - - -
127N GLN* 6.0 0.2 + - - -
130N ARG* 4.5 4.6 + - - -
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Residues in contact with GLY 311 (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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307L ALA 3.6 3.5 + - - +
308L GLU* 3.2 19.5 + - - +
310L MET* 1.3 82.3 - - - +
312L PRO* 1.3 76.3 - - - +
313L GLY 3.7 0.5 + - - -
314L TRP* 3.6 17.9 + - - +
126N ARG* 4.7 0.4 - - - -
130N ARG* 4.3 13.0 - - - -
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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