Contacts of the strand formed by residues 249 - 255 (chain A) in PDB entry 4CAA
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 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A GLU* 3.1 28.5 + - - +
242A LEU 3.8 9.4 - - - -
243A LYS* 3.9 11.2 - - - -
244A TYR* 3.7 11.2 - - - -
248A ALA* 1.3 76.9 - - - +
250A ALA* 1.3 59.8 + - - +
251A LEU* 4.1 0.6 - - - +
276A ARG* 4.0 3.5 + - - -
374B ILE* 3.3 6.4 - - - +
375B VAL* 2.7 57.0 + - - +
376B PRO 5.0 0.5 + - - -
377B THR* 4.9 5.7 + - - -
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Residues in contact with ALA 250 (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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194A TRP* 4.2 1.8 - - + -
241A GLU* 3.7 4.0 - - - +
242A LEU 3.0 35.7 + - - +
244A TYR* 3.3 26.9 - - + +
249A SER* 1.3 73.0 - - - +
251A LEU* 1.3 62.3 + - - +
252A PHE* 3.8 25.6 + - + -
372B MET* 4.1 11.9 - - + -
373B ILE 3.5 5.2 - - - +
374B ILE* 4.5 0.9 - - + +
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Residues in contact with LEU 251 (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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239A VAL* 3.9 25.6 - - + -
240A VAL 3.7 5.2 - - - +
241A GLU* 4.8 7.0 - - + -
249A SER 4.1 0.6 - - - -
250A ALA* 1.3 71.2 - - - +
252A PHE* 1.3 61.8 + - - +
253A ILE* 3.8 8.7 - - + +
272A LEU* 3.8 28.7 - - + -
275A TRP* 5.5 2.0 - - + -
276A ARG* 3.9 20.4 - - + +
278A LEU* 4.0 20.6 - - + -
372B MET* 3.2 4.2 - - - +
373B ILE* 2.8 39.5 + - + +
375B VAL* 3.6 35.0 - - + -
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Residues in contact with PHE 252 (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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194A TRP* 4.3 6.3 - + - -
238A THR 3.6 1.4 - - - +
239A VAL* 3.4 5.2 - - - +
240A VAL* 3.1 36.5 + - + +
242A LEU* 4.1 29.2 - - + -
250A ALA* 3.8 25.1 - - + -
251A LEU* 1.3 71.3 - - - +
253A ILE* 1.3 64.7 + - - +
254A LEU 4.1 0.4 - - - -
288A LEU* 3.7 38.4 - - + -
291A PHE* 5.6 1.3 - + - -
340A VAL* 5.5 0.7 - - + -
366B PHE* 3.4 25.7 - + + -
370B PHE* 4.3 10.3 - + - -
371B LEU 3.5 12.3 - - - -
372B MET* 3.2 42.2 - - + -
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Residues in contact with ILE 253 (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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237A CYS* 3.9 31.9 - - + -
238A THR 3.6 4.3 - - - +
239A VAL* 4.4 10.8 - - + -
251A LEU* 3.8 20.2 - - + +
252A PHE* 1.3 79.9 - - - +
254A LEU* 1.3 60.0 + - - +
255A PRO* 2.9 21.7 - - + +
263A VAL* 4.3 5.8 - - + -
272A LEU* 6.4 0.2 - - + -
275A TRP* 3.9 31.0 - - + -
366B PHE* 4.4 0.4 - - - -
370B PHE* 4.3 1.6 - - - -
371B LEU* 2.9 44.2 + - + -
373B ILE* 4.4 19.7 - - + -
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Residues in contact with LEU 254 (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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237A CYS* 3.7 2.7 - - - -
238A THR* 3.1 37.2 + - - +
253A ILE* 1.3 70.6 - - - +
255A PRO* 1.3 65.8 - - - +
256A ASP* 3.6 1.9 + - - +
364B VAL* 5.3 4.0 - - + -
365B ARG 3.5 32.1 - - - +
366B PHE* 3.6 26.7 - - + -
368B ARG* 3.6 63.0 + - + +
369B PRO 3.7 6.1 - - - +
370B PHE* 3.9 8.1 - - + -
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Residues in contact with PRO 255 (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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236A SER 4.1 0.2 - - - +
237A CYS* 3.7 10.7 - - + -
253A ILE* 2.9 22.9 - - + +
254A LEU* 1.3 78.6 - - - +
256A ASP* 1.3 66.5 + - - +
260A MET* 3.6 41.1 - - + +
263A VAL* 3.7 31.2 - - + -
368B ARG* 2.9 19.4 + - - +
369B PRO 3.7 17.9 - - - +
370B PHE* 3.9 3.1 - - - -
371B LEU* 5.0 1.1 - - + -
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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