Contacts of the strand formed by residues 428 - 434 (chain B) in PDB entry 2R5N
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 LEU 428 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333B MET* 4.6 4.3 - - - -
372B LEU* 4.5 11.7 - - + -
374B GLU* 2.8 24.3 + - + +
375B PHE* 3.4 19.1 - - + -
376B LEU 3.0 18.9 + - - -
427B PHE* 1.3 72.9 - - - +
429B PRO* 1.3 81.3 - - + +
430B TYR* 3.7 0.9 + - + -
454B ARG* 3.4 39.7 - - + +
456B VAL* 4.2 21.5 - - + +
507B VAL* 3.7 35.0 - - + +
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Residues in contact with PRO 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B LEU* 3.2 14.4 - - - +
407B TYR* 5.6 0.4 - - - +
418B ALA* 3.6 37.0 - - + +
421B ILE* 4.0 15.7 - - + -
422B SER* 4.0 12.3 - - - +
427B PHE 3.9 6.9 - - - +
428B LEU* 1.3 92.0 - - + +
430B TYR* 1.3 59.3 + - - +
431B THR* 5.3 0.2 - - + -
454B ARG* 3.6 22.9 - - - +
455B GLN* 3.4 9.2 - - + +
456B VAL 3.1 21.1 + - - -
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Residues in contact with TYR 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B ILE* 3.6 23.3 - - + +
375B PHE* 4.0 36.8 - + + -
376B LEU 3.4 5.7 + - - +
377B GLY* 3.2 26.5 - - - -
378B GLY* 3.0 33.6 + - - -
388B THR* 2.7 44.2 + - + -
390B TRP* 4.2 7.5 + - - -
393B SER* 4.4 0.2 + - - -
403B ASN 5.3 1.5 + - - -
404B TYR* 4.2 6.6 - - - -
407B TYR* 4.7 1.2 + - - -
428B LEU* 5.5 0.4 - - + -
429B PRO* 1.3 73.7 - - - +
431B THR* 1.3 67.5 + - - +
455B GLN* 4.8 0.4 - - - -
456B VAL* 3.1 16.2 - - + +
458B VAL* 4.4 10.3 - - + -
503B TRP* 3.9 26.9 - + + -
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Residues in contact with THR 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B GLY 3.5 6.1 - - - -
407B TYR* 4.4 6.1 - - + +
414B MET* 3.7 31.8 - - + +
415B THR* 4.5 5.2 + - - -
418B ALA* 3.4 22.2 - - + -
429B PRO* 5.3 0.2 - - + -
430B TYR* 1.3 80.8 - - - +
432B SER* 1.3 64.7 + - - +
455B GLN* 2.8 29.8 + - - +
456B VAL 3.0 3.0 + - - -
457B MET* 3.9 11.8 - - - +
458B VAL* 2.8 28.3 + - - +
459B TYR* 4.9 3.4 + - - -
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Residues in contact with SER 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B GLY 3.3 7.5 + - - -
379B SER* 3.5 1.5 - - - -
380B ALA 3.0 26.5 + - - -
386B ASN* 3.0 28.0 + - - +
388B THR* 3.4 24.2 - - - -
414B MET* 3.3 8.8 - - - +
431B THR* 1.3 81.5 - - - +
433B THR* 1.3 63.5 + - - +
458B VAL* 2.6 27.5 + - - +
459B TYR* 5.0 2.5 - - - -
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Residues in contact with THR 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B ALA* 4.5 4.1 - - - +
382B LEU* 3.8 12.4 - - - +
386B ASN* 3.3 15.4 + - - +
411B GLU* 3.7 36.2 + - + +
414B MET* 4.4 5.2 - - + -
432B SER* 1.3 78.2 + - - +
434B PHE* 1.3 82.8 + - - +
437B PHE* 3.8 18.1 - - - +
438B VAL* 4.9 0.4 - - - -
441B ALA* 6.2 0.4 - - + -
458B VAL 3.3 6.1 + - - +
459B TYR* 3.4 22.3 - - + -
460B THR 3.3 18.0 + - - -
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Residues in contact with PHE 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672A TPP 4.1 10.3 - - - -
382B LEU* 3.7 34.2 - - + +
385B SER* 4.0 5.4 - - - -
386B ASN* 3.7 7.0 - - - -
433B THR* 1.3 89.5 + - - +
435B LEU* 1.3 67.7 + - - +
436B MET* 4.3 4.7 - - + +
437B PHE* 2.9 42.9 + + + -
460B THR* 3.5 9.6 - - - +
461B HIS* 3.3 56.8 - + + +
466B LEU* 6.4 0.2 - - + -
469B ASP* 4.9 0.7 - - - -
473B HIS* 4.1 20.9 - + + +
681B RP5 4.1 23.8 - - - -
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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