Contacts of the helix formed by residues 301 - 308 (chain L) in PDB entry 3CX5
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 LYS 301 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121G ASP* 3.2 31.0 + - - +
122G ASN* 4.8 3.8 + - - -
299L GLY 4.3 1.8 + - - +
300L ILE* 1.3 70.6 - - - +
302L LEU* 1.3 65.2 + - - +
304L ASP* 3.0 30.3 + - - +
305L ASN* 3.9 5.9 + - - +
350L GLN* 3.8 20.1 - - - +
353L ARG* 3.8 19.5 - - - +
359L THR* 4.8 8.7 - - - -
362L GLU* 3.7 37.3 + - + +
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Residues in contact with LEU 302 (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 PHE* 5.1 4.7 - - + -
300L ILE* 3.2 14.1 - - + +
301L LYS* 1.3 76.7 - - - +
303L LEU* 1.3 63.0 + - - +
305L ASN* 3.0 16.7 + - - +
306L ILE* 3.2 22.3 + - + +
315L PHE* 4.0 29.4 - - + -
317L HIS* 4.4 8.7 - - + +
330L PHE* 5.9 0.2 - - + -
343L LEU* 6.0 0.2 - - + -
346L PHE* 3.6 43.3 - - + +
347L THR* 3.7 26.9 - - + +
350L GLN* 3.7 24.1 - - + +
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Residues in contact with LEU 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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288L TYR* 3.6 35.0 - - + -
295L SER 3.5 24.2 - - - +
296L ARG 4.2 9.2 - - - +
298L GLN* 4.0 27.1 - - + +
300L ILE* 3.0 27.1 + - + +
302L LEU* 1.3 77.9 - - - +
304L ASP* 1.3 61.9 + - - +
306L ILE* 3.8 10.3 - - + -
307L GLN* 3.2 37.9 + - - +
315L PHE* 3.8 20.9 - - + -
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Residues in contact with ASP 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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117G LYS* 3.0 34.5 + - - -
121G ASP* 3.9 8.7 - - - +
300L ILE 5.1 1.9 - - - +
301L LYS* 3.0 22.8 + - - +
303L LEU* 1.3 81.2 - - - +
305L ASN* 1.3 67.8 + - - +
307L GLN* 4.2 5.5 + - - +
308L GLU* 4.3 12.0 + - - +
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Residues in contact with ASN 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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301L LYS 4.1 7.9 - - - +
302L LEU* 3.0 10.3 + - - +
304L ASP* 1.3 83.7 - - - +
306L ILE* 1.3 61.5 + - - +
308L GLU* 4.3 12.4 + - - +
309L TYR* 5.1 1.6 + - - -
311L LEU* 4.0 3.1 - - - +
346L PHE* 3.7 58.9 - - + +
350L GLN* 3.9 18.4 - - - +
1N MET 5.2 3.3 + - - -
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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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288L TYR* 4.0 7.0 - - + -
302L LEU* 3.2 33.2 + - + +
303L LEU* 3.8 17.0 - - + -
304L ASP 3.5 0.2 - - - -
305L ASN* 1.3 80.0 - - + +
307L GLN* 1.3 62.7 + - + +
308L GLU 3.5 0.4 - - - -
309L TYR 4.2 0.8 + - - -
310L GLN* 3.3 7.2 + - - +
311L LEU* 2.9 57.3 + - + +
312L CYS* 4.0 15.7 - - - +
315L PHE* 3.5 37.7 - - + -
343L LEU* 4.4 11.2 - - + -
346L PHE* 4.5 4.0 - - + -
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Residues in contact with GLN 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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288L TYR* 2.9 35.9 + - + +
296L ARG* 3.1 47.3 + - - +
303L LEU* 3.2 28.9 + - - +
304L ASP* 4.2 2.9 + - - +
305L ASN 3.6 0.2 - - - -
306L ILE* 1.3 80.5 - - + +
308L GLU* 1.3 67.5 + - - +
310L GLN* 3.2 23.5 + - - +
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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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7H LYS* 3.5 23.3 + - - +
304L ASP 4.3 9.5 + - - +
305L ASN 4.3 10.6 + - - +
306L ILE 3.5 1.0 - - - -
307L GLN* 1.3 78.7 - - - +
309L TYR* 1.3 88.1 + - + +
1N MET 4.5 7.1 + - - -
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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