Contacts of the strand formed by residues 373 - 380 (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 TRP 373 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263D ALA* 4.2 23.8 + - + -
266D THR* 3.1 55.8 + - + +
268D THR 4.7 1.8 + - - -
269D VAL* 3.4 24.8 - - + +
273D PHE* 4.4 9.9 - + - -
277D LEU* 3.6 32.1 - - + -
279D SER* 3.8 16.2 - - - -
365D ILE* 3.5 39.0 - - + -
366D LEU 3.6 5.4 - - - -
367D LEU* 3.3 44.6 - - + -
372D LYS* 1.3 75.4 - - - +
374D GLU* 1.3 59.8 + - - +
375D ARG* 4.3 2.1 + - - +
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Residues in contact with GLU 374 (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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365D ILE* 3.3 4.5 - - - -
366D LEU* 2.8 44.5 + - + +
368D ASN* 4.3 18.2 - - + +
373D TRP* 1.3 74.4 - - - +
375D ARG* 1.3 65.5 + - - +
376D VAL* 3.4 10.8 + - + +
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Residues in contact with ARG 375 (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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283D ASP* 5.2 4.2 - - - +
285D TRP* 4.0 27.3 - - - +
362D LEU 5.3 0.4 + - - -
363D VAL* 3.5 29.5 - - + +
364D ILE 4.0 5.2 - - - +
365D ILE* 4.3 11.9 - - + -
373D TRP 4.3 2.0 + - - +
374D GLU* 1.3 74.5 - - - +
376D VAL* 1.3 63.3 + - - +
377D GLY 3.8 11.2 + - - +
378D LYS* 4.8 9.1 - - - +
387D LYS* 5.4 0.7 - - - +
388D TYR* 5.6 0.9 + - - -
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Residues in contact with VAL 376 (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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364D ILE* 2.9 27.4 + - + +
365D ILE 4.0 0.9 - - - -
366D LEU* 3.6 28.9 - - + +
374D GLU* 3.5 15.9 - - + +
375D ARG* 1.3 79.3 - - - +
377D GLY* 1.3 58.8 + - - +
386D MET* 3.9 7.3 - - - +
387D LYS* 3.2 32.2 + - - +
388D TYR* 4.0 29.2 + - + +
391D TRP* 3.8 25.1 - - + -
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Residues in contact with GLY 377 (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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363D VAL* 3.5 7.8 - - - +
364D ILE* 2.9 37.8 + - - +
375D ARG* 3.8 8.5 + - - +
376D VAL* 1.3 81.5 + - - +
378D LYS* 1.3 61.9 + - - +
385D GLN 3.8 7.9 - - - -
386D MET* 4.3 7.2 - - - -
387D LYS* 4.3 2.0 - - - -
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Residues in contact with LYS 378 (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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362D LEU 3.6 7.6 - - - +
364D ILE* 3.8 6.4 - - - +
375D ARG* 4.8 10.1 - - - +
377D GLY* 1.3 74.6 - - - +
379D TRP* 1.3 61.4 + - - +
380D LYS* 5.6 4.7 - - + +
383D SER 4.1 0.5 - - - +
384D LEU* 3.8 1.2 - - - +
385D GLN* 2.9 58.4 + - + +
386D MET* 5.4 0.2 - - - +
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Residues in contact with TRP 379 (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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152D GLN* 3.3 17.3 - - + +
155D SER* 4.4 7.0 - - - -
156D VAL* 3.6 28.2 - - + +
159D ASN* 3.2 28.9 - - - -
360D PRO 4.2 3.8 - - - -
361D LYS* 3.8 3.6 - - - +
362D LEU* 2.8 68.5 + - + +
364D ILE* 3.8 11.5 - - + +
378D LYS* 1.3 73.5 - - - +
380D LYS* 1.3 58.8 + - - +
381D ASP 2.6 35.1 + - - -
382D LYS* 3.6 19.7 - - + -
383D SER 3.8 2.7 - - - -
384D LEU* 3.4 39.0 - - + -
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Residues in contact with LYS 380 (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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361D LYS* 5.5 2.9 - - - +
378D LYS* 4.1 5.7 - - + -
379D TRP* 1.3 69.8 - - - +
381D ASP* 1.3 58.7 + - - +
382D LYS 2.5 18.5 + - - -
383D SER* 2.9 32.3 + - - +
385D GLN* 6.5 0.9 - - + -
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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