Contacts of the strand formed by residues 361 - 367 (chain D) in PDB entry 4PE5
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 361 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282D TYR* 3.8 9.8 - - + -
283D ASP* 3.6 27.8 + - + +
359D HIS 3.8 2.0 + - - -
360D PRO* 1.3 70.2 - - - +
362D LEU* 1.3 65.9 + - - +
379D TRP 3.8 7.0 - - - +
380D LYS* 5.8 2.0 - - - -
381D ASP 5.2 2.9 - - - +
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Residues in contact with LEU 362 (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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148D PRO* 3.6 44.2 - - + -
152D GLN* 4.6 4.3 - - + +
153D GLN* 5.2 0.9 - - - -
156D VAL* 3.9 16.4 - - + -
280D VAL* 3.7 23.3 - - + -
281D SER 3.8 10.1 - - - +
282D TYR* 4.5 3.6 - - + -
283D ASP* 4.7 2.2 - - - +
360D PRO* 3.7 15.3 - - + +
361D LYS* 1.3 82.6 - - - +
363D VAL* 1.3 60.3 + - - +
364D ILE* 5.3 0.7 - - + -
375D ARG* 5.3 0.2 + - - -
378D LYS* 3.6 5.2 - - - +
379D TRP* 2.8 64.5 + - + +
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Residues in contact with VAL 363 (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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280D VAL* 3.6 1.1 - - - -
281D SER* 2.9 44.2 + - - +
283D ASP* 4.4 13.6 - - + +
361D LYS 4.3 0.2 + - - -
362D LEU* 1.3 76.5 - - - +
364D ILE* 1.3 62.9 + - - +
365D ILE* 4.8 9.0 - - + -
375D ARG* 3.5 34.5 - - - +
377D GLY 3.5 4.9 - - - +
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Residues in contact with ILE 364 (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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156D VAL* 4.4 11.9 - - + -
160D ILE* 3.6 35.7 - - + -
278D ILE* 3.9 17.5 - - + -
279D SER 3.6 6.3 - - - +
280D VAL* 5.3 4.3 - - + -
362D LEU* 4.9 1.1 - - + -
363D VAL* 1.3 72.4 - - - +
365D ILE* 1.3 61.3 + - - +
375D ARG* 3.9 0.9 - - - -
376D VAL* 2.9 36.9 + - + +
377D GLY* 2.9 27.2 + - - +
378D LYS 3.8 7.6 - - - +
379D TRP* 3.8 34.8 - - + +
384D LEU* 6.0 2.0 - - + -
386D MET* 4.2 15.5 - - + -
391D TRP* 5.2 0.4 - - + -
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Residues in contact with ILE 365 (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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263D ALA* 4.0 7.2 - - + -
266D THR* 3.7 23.6 - - + -
278D ILE* 3.5 5.7 - - - +
279D SER* 2.9 54.8 + - - +
281D SER* 3.6 28.7 - - - -
363D VAL* 4.4 7.4 - - + +
364D ILE* 1.3 78.4 - - - +
366D LEU* 1.3 61.9 + - - +
373D TRP* 3.5 29.3 - - + -
374D GLU 3.3 13.7 - - - +
375D ARG* 4.3 15.7 - - + -
376D VAL* 4.0 1.6 - - - -
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Residues in contact with LEU 366 (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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276D GLY* 3.4 28.0 - - - +
277D LEU 3.3 16.2 - - - +
278D ILE* 3.8 2.9 - - + -
365D ILE* 1.3 75.7 - - - +
367D LEU* 1.3 66.2 + - - +
368D ASN* 3.3 6.7 + - + +
373D TRP* 3.6 3.8 - - - -
374D GLU* 2.8 35.2 + - + +
376D VAL* 3.6 28.0 - - + -
388D TYR* 5.5 0.4 - - + -
391D TRP* 3.5 35.0 - - + +
392D PRO* 5.0 17.0 - - + +
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Residues in contact with LEU 367 (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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269D VAL* 3.7 22.7 - - + -
273D PHE* 3.8 28.7 - - + +
274D PRO 3.2 25.1 - - - +
275D THR* 4.1 1.5 - - - +
276D GLY* 2.8 31.5 + - - -
277D LEU* 2.8 23.2 + - + +
366D LEU* 1.3 71.3 - - - +
368D ASN* 1.3 65.0 + - - +
371D ARG* 3.6 36.3 - - - +
372D LYS 3.9 8.3 - - - +
373D TRP* 3.3 22.7 - - + -
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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