Contacts of the strand formed by residues 304 - 308 (chain A) in PDB entry 3CXM
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 VAL 304 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A LYS 2.9 11.4 + - - +
200A VAL* 3.2 4.1 - - + +
201A VAL* 2.9 25.6 + - - +
303A LEU* 1.3 73.2 - - - +
305A PHE* 1.3 62.1 + - - +
306A LEU* 3.7 23.6 - - + -
325A VAL* 3.3 10.5 - - + +
327A LEU* 3.9 19.5 - - + -
350A CYS* 4.0 12.6 - - - -
353A ALA* 3.9 16.4 - - + -
354A LEU* 3.7 20.6 - - + -
357A MET* 3.7 26.0 - - - -
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Residues in contact with PHE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A VAL* 3.3 34.8 - - + -
203A LEU* 5.4 2.2 - - + -
292A ILE* 4.3 14.8 - - + -
295A LEU* 4.9 4.5 - - + -
296A SER* 4.8 13.5 - - - -
303A LEU* 3.8 33.4 - - + -
304A VAL* 1.3 74.9 - - - +
306A LEU* 1.3 62.5 + - - +
307A LEU* 3.8 10.8 + - + -
319A ILE* 3.6 56.1 - - + -
324A HIS* 3.8 14.8 - + + -
325A VAL 2.8 17.4 + - - +
326A VAL* 3.5 6.1 - - + +
327A LEU* 2.9 28.9 + - - +
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Residues in contact with LEU 306 (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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200A VAL* 3.8 26.5 - - + -
201A VAL 2.8 9.8 + - - +
202A LEU* 3.7 16.4 - - + +
203A LEU 3.6 22.7 + - - -
261A MET* 4.1 15.9 - - + -
304A VAL* 3.7 23.6 - - + -
305A PHE* 1.3 74.5 - - - +
307A LEU* 1.3 63.6 + - - +
308A TRP* 3.9 27.5 + - + +
327A LEU* 3.5 22.7 - - + +
346A CYS* 4.8 7.4 - - + +
347A PHE* 5.5 1.8 - - + -
350A CYS* 4.2 15.9 - - + -
364A TRP* 4.6 7.6 - - + -
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Residues in contact with LEU 307 (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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203A LEU* 3.5 33.9 - - + -
305A PHE* 4.3 14.6 - - + +
306A LEU* 1.3 78.8 - - - +
308A TRP* 1.3 60.7 + - - +
309A GLY 4.0 0.2 - - - -
312A ALA* 3.8 21.5 - - + +
313A GLN* 3.4 21.4 + - + -
315A LYS* 5.0 0.2 - - + -
316A LYS* 4.0 25.8 - - + +
319A ILE* 4.2 7.9 - - + -
326A VAL* 3.4 31.2 - - + -
327A LEU 3.0 11.6 + - - +
328A GLU* 3.3 6.1 - - + -
329A ASN 3.0 25.1 + - - +
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Residues in contact with TRP 308 (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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202A LEU* 3.7 40.8 - - + -
203A LEU 5.1 5.1 + - - +
219A PHE* 4.0 14.6 - + + -
234A ILE* 3.7 30.1 - - + -
256A TRP* 5.9 1.8 - + - -
261A MET* 5.9 0.4 - - + -
306A LEU* 3.9 22.3 + - + +
307A LEU* 1.3 83.1 - - - +
309A GLY* 1.3 63.6 + - - +
311A TYR* 5.9 0.3 - - - +
312A ALA* 3.6 15.5 + - - +
327A LEU 4.8 0.9 + - - -
329A ASN* 3.2 21.5 + - + +
330A VAL 4.3 1.1 - - - +
331A HIS* 3.4 16.6 - - + -
332A PRO* 4.0 25.6 - - + -
341A TRP* 3.7 26.5 - + - -
346A CYS* 4.0 14.6 - - - +
347A PHE* 3.9 26.9 - + - -
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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