Contacts of the strand formed by residues 252 - 256 (chain D) in PDB entry 4P0S
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 ILE 252 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248D CYS 3.3 17.3 - - - +
249D LEU* 3.3 17.5 + - + +
250D LYS 3.5 1.5 - - - -
251D HIS* 1.3 91.5 - - - +
253D ILE* 1.3 66.5 + - - +
254D VAL* 4.9 3.8 - - + +
278D CYS* 3.8 9.3 - - + +
279D ARG 3.6 9.9 + - - +
293D TRP* 3.8 32.3 - - + -
294D ARG 3.5 4.3 - - - +
295D ARG* 3.4 53.6 - - + +
309D GLU* 5.6 0.7 - - + -
440D THR* 5.0 7.6 - - + -
443D VAL* 5.4 0.9 - - + -
444D ALA* 4.2 17.3 - - + -
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Residues in contact with ILE 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252D ILE* 1.3 76.9 - - - +
254D VAL* 1.3 62.6 + - - +
255D VAL* 3.5 4.0 + - + +
279D ARG* 3.1 35.2 - - + +
281D VAL* 4.1 27.1 - - + -
293D TRP* 3.6 4.7 - - - -
294D ARG* 3.1 64.8 + - + +
301D GLU* 6.1 0.2 - - - +
306D TRP* 3.9 31.9 - - + -
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Residues in contact with VAL 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252D ILE* 4.9 2.9 - - + +
253D ILE* 1.3 74.5 - - - +
255D VAL* 1.3 60.1 + - - +
256D LEU* 3.0 29.7 - - + +
273D LEU* 3.8 23.6 - - + -
278D CYS* 4.8 4.9 - - - -
279D ARG 3.3 6.3 + - - +
280D CYS* 3.6 12.5 - - - -
281D VAL 3.0 19.4 + - - -
291D VAL* 3.9 20.9 - - + -
292D THR 4.0 2.0 - - - -
293D TRP* 4.0 12.8 - - + +
436D THR* 6.3 0.4 - - + -
440D THR* 3.9 29.4 - - + +
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Residues in contact with VAL 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D ILE* 4.2 5.2 - - + +
254D VAL* 1.3 69.5 - - - +
256D LEU* 1.3 65.1 + - - +
281D VAL* 3.5 28.5 - - + +
283D GLU* 4.6 6.3 - - + +
285D GLN* 3.4 32.8 - - - +
290D SER 4.0 1.0 - - - +
291D VAL* 3.4 7.3 - - - +
292D THR* 3.2 40.1 + - - +
294D ARG* 3.6 44.6 - - + +
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Residues in contact with LEU 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254D VAL* 3.0 46.0 - - + +
255D VAL* 1.3 76.1 - - - +
257D ASP* 1.3 67.9 + - - +
260D LEU* 3.5 23.8 - - + -
261D LEU* 4.5 20.2 - - + -
269D LEU* 4.6 18.4 - - + -
270D LEU* 4.3 22.7 - - + -
273D LEU* 4.8 3.4 - - + -
280D CYS* 4.5 1.3 - - + -
281D VAL 2.9 9.8 + - - +
282D ILE* 3.5 12.1 - - + +
283D GLU 3.4 24.0 + - - +
285D GLN* 5.6 0.7 - - - -
290D SER 4.2 2.5 - - - -
291D VAL* 4.5 7.4 - - + -
436D THR* 6.2 0.4 - - + -
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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