Contacts of the helix formed by residues 280 - 287 (chain A) in PDB entry 3CXW
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 THR 280 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A VAL* 5.1 1.1 - - - -
278A ARG 3.8 1.1 + - - +
279A PRO* 1.3 76.4 - - - +
281A PHE* 1.3 66.8 + - - +
282A GLU* 3.6 10.9 + - - +
283A GLU* 2.8 41.4 + - - +
284A ILE* 3.0 23.2 + - - +
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Residues in contact with PHE 281 (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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152A LEU* 3.9 17.3 - - + -
155A VAL* 3.6 17.0 - - + -
156A ARG* 3.7 37.7 - - + +
159A HIS* 3.3 46.0 - + + -
221A ARG* 4.9 6.3 - - + -
224A ALA* 4.5 4.5 - - + -
225A VAL* 3.8 25.8 - - + -
228A LEU* 3.8 16.6 - - + -
280A THR* 1.3 72.6 - - - +
282A GLU* 1.3 57.7 + - - +
284A ILE* 3.3 6.0 + - + +
285A GLN* 2.9 35.2 + - - +
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Residues in contact with GLU 282 (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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280A THR* 3.2 10.2 + - - +
281A PHE* 1.3 78.7 - - - +
283A GLU* 1.3 57.6 + - + +
285A GLN* 3.3 6.0 + - - +
286A ASN* 3.0 48.4 + - - +
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Residues in contact with GLU 283 (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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269A TRP* 3.6 35.2 - - + -
278A ARG 4.3 1.6 - - - +
279A PRO* 3.2 14.1 - - + +
280A THR* 2.8 45.7 + - - +
282A GLU* 1.3 73.2 - - + +
284A ILE* 1.3 65.2 + - - +
286A ASN* 3.4 5.6 + - - +
287A HIS* 3.0 22.7 + - - +
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Residues in contact with ILE 284 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A PHE* 3.9 17.0 - - + -
152A LEU* 3.9 23.1 - - + -
225A VAL* 4.0 25.4 - - + -
228A LEU* 4.8 7.2 - - + -
266A LEU* 4.2 14.8 - - + -
270A CYS* 4.0 20.0 - - - -
279A PRO* 3.6 17.0 - - + -
280A THR 3.0 19.2 + - - +
281A PHE* 3.3 8.5 + - + +
283A GLU* 1.3 75.0 - - - +
285A GLN* 1.3 59.9 + - - +
287A HIS* 3.1 23.9 + - - +
290A MET* 3.1 31.8 - - + +
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Residues in contact with GLN 285 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A TRP* 3.5 54.9 - - + -
152A LEU* 4.0 25.0 - - + +
153A GLU* 2.8 28.8 + - - +
156A ARG* 3.1 37.0 + - - -
281A PHE 2.9 20.1 + - - +
282A GLU* 3.3 5.8 + - - +
284A ILE* 1.3 76.2 - - - +
286A ASN* 1.3 61.4 + - - +
287A HIS 4.4 0.3 - - - +
290A MET* 3.8 11.7 - - + +
291A GLN* 5.8 1.0 - - - +
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Residues in contact with ASN 286 (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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282A GLU* 3.0 42.8 + - - +
283A GLU* 3.7 6.0 - - - +
285A GLN* 1.3 77.9 - - - +
287A HIS* 1.3 65.4 + - - +
288A PRO* 3.6 4.7 - - - +
291A GLN* 5.2 4.2 - - - +
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Residues in contact with HIS 287 (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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262A GLU* 3.1 35.4 - - - -
265A HIS* 2.8 31.8 + + - -
266A LEU* 3.7 31.7 + - + +
269A TRP* 3.9 16.4 - + - -
283A GLU 3.0 10.2 + - - +
284A ILE 3.1 18.0 + - - +
285A GLN 4.4 0.2 - - - +
286A ASN* 1.3 79.0 - - - +
288A PRO* 1.3 83.2 - - + +
289A TRP* 3.0 29.1 + - - +
290A MET* 2.9 18.4 + - + +
291A GLN* 3.8 5.2 + - - +
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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