Contacts of the strand formed by residues 412 - 418 (chain B) in PDB entry 4R95
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 ARG 412 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251B TYR* 3.5 49.1 + - + -
252B THR 3.3 13.9 - - - +
253B PRO* 4.4 0.4 - - + -
254B ILE* 3.5 5.1 - - - +
351B GLU* 2.8 40.8 + - - +
407B ASP* 2.8 59.8 + - + +
410B ARG* 3.4 54.4 - - - +
411B LYS* 1.3 78.2 - - - +
413B ILE* 1.3 66.9 + - - +
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Residues in contact with ILE 413 (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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250B TRP 3.8 0.9 - - - +
251B TYR* 3.3 3.7 - - - -
252B THR* 2.8 40.9 + - + +
254B ILE* 3.7 20.9 - - + -
260B TYR* 3.6 31.4 - - + -
262B VAL* 3.8 19.5 - - + -
288B VAL* 4.3 8.3 - - + -
404B VAL* 3.6 24.5 - - + -
405B VAL 3.1 7.4 - - - +
406B PHE* 4.2 12.1 - - + -
412B ARG* 1.3 78.3 - - - +
414B GLY* 1.3 61.3 + - - +
415B PHE* 3.5 25.3 - - + -
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Residues in contact with GLY 414 (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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249B LEU* 3.9 7.6 - - - -
250B TRP 3.3 8.7 - - - -
251B TYR* 3.3 22.6 - - - -
403B TYR 3.6 0.2 - - - +
404B VAL* 3.4 11.1 - - - +
405B VAL* 2.8 36.2 + - - -
413B ILE* 1.3 74.1 - - - +
415B PHE* 1.4 61.8 + - - -
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Residues in contact with PHE 415 (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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249B LEU* 3.5 3.8 - - - +
250B TRP 2.8 30.4 + - - +
252B THR* 4.1 7.9 - - + -
262B VAL* 5.5 0.4 - - + -
288B VAL* 4.2 13.0 - - + -
348B LEU* 3.6 23.8 - - + -
357B PHE* 4.1 6.1 - + + -
359B ILE* 3.9 31.4 - - + -
394B MET* 3.7 32.5 - - + -
398B ILE* 5.7 0.4 - - + -
399B MET* 6.0 1.8 - - + -
402B PHE* 4.1 20.2 - + + -
403B TYR 3.5 2.9 - - - -
404B VAL* 4.1 17.5 - - + -
413B ILE* 3.5 30.7 - - + -
414B GLY* 1.4 77.0 - - - -
416B ALA* 1.3 61.2 + - - +
431B VAL* 3.3 13.6 - - + +
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Residues in contact with ALA 416 (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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245B TYR* 3.5 37.5 - - + -
246B THR 4.2 1.1 - - - +
248B SER 3.7 14.1 - - - +
249B LEU* 3.8 12.8 - - + -
402B PHE* 3.2 5.5 - - - +
403B TYR* 2.8 31.5 + - + +
415B PHE* 1.3 75.9 - - - +
417B VAL* 1.4 61.6 - - - +
431B VAL* 3.7 9.2 - - - -
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Residues in contact with VAL 417 (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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245B TYR* 3.3 5.9 - - - -
246B THR* 3.1 50.9 + - - +
247B GLY* 6.4 0.2 - - - -
248B SER 5.1 0.4 + - - -
401B GLY 4.0 4.9 - - - +
402B PHE* 4.3 2.7 - - + -
416B ALA* 1.4 71.2 - - - +
418B SER* 1.3 65.1 + - - +
421B HIS* 3.6 31.9 - - + +
428B THR* 4.7 1.1 - - - +
429B ALA 3.7 7.6 - - - +
430B ALA* 3.6 31.4 - - - -
431B VAL* 3.7 12.5 - - + +
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Residues in contact with SER 418 (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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214B GLN* 3.6 10.4 - - - +
215B LEU 4.9 0.4 + - - -
244B LEU 3.8 4.9 - - - -
246B THR* 5.0 0.8 + - - -
400B GLU 4.1 3.4 - - - -
401B GLY 3.0 25.1 + - - -
402B PHE 3.7 17.3 - - - -
403B TYR 3.9 3.8 - - - +
416B ALA 3.3 1.8 + - - -
417B VAL* 1.3 74.4 - - - +
419B ALA* 1.3 62.4 + - - +
420B CYS* 3.0 31.0 + - - -
421B HIS* 3.2 26.2 + - - -
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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