Contacts of the strand formed by residues 218 - 222 (chain B) in PDB entry 3HNF
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 CYS 218 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B SER 3.7 0.2 - - - -
217B SER* 1.3 87.3 + - - +
219B PHE* 1.3 63.9 + - - +
220B LEU* 4.7 1.6 - - + -
247B GLY* 3.6 15.5 - - - -
427B ASN* 3.2 40.2 - - + +
428B LEU* 4.6 7.9 - - - -
429B CYS* 5.0 5.8 - - - -
431B GLU* 5.5 0.4 - - - -
432B ILE* 4.8 9.6 - - + -
442B ALA 4.4 0.2 - - - -
443B VAL* 3.2 5.9 - - - +
444B CYS* 2.7 36.7 + - + +
446B LEU* 5.4 7.0 - - + -
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Residues in contact with PHE 219 (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* 5.2 3.8 - - - -
216B SER* 3.5 26.5 - - - -
217B SER 3.9 3.1 - - - -
218B CYS* 1.3 77.9 - - - +
220B LEU* 1.3 65.5 + - - +
221B LEU* 4.7 2.7 - - + -
241B ILE* 3.4 36.3 - - + -
244B SER* 5.6 1.8 - - - -
246B GLY* 3.8 13.9 - - - -
247B GLY 3.0 13.0 + - - +
248B ILE* 3.4 6.9 - - + -
249B GLY 3.1 22.5 + - - +
427B ASN* 4.6 2.8 - - - +
441B VAL* 4.3 12.3 - - + -
442B ALA 3.2 6.1 - - - -
443B VAL* 3.5 38.4 - - + -
484B ASN* 5.3 1.8 - - - -
486B TYR* 5.2 0.7 - + - -
487B PRO* 3.5 35.4 - - + -
491B ALA* 4.4 1.1 - - + -
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Residues in contact with LEU 220 (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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218B CYS* 4.7 2.9 - - + +
219B PHE* 1.3 82.0 - - - +
221B LEU* 1.3 61.5 + - - +
249B GLY 3.5 5.8 - - - +
425B CYS* 3.7 17.5 - - - +
426B SER* 3.5 33.2 - - - +
427B ASN* 3.9 9.0 - - + +
432B ILE* 3.6 33.2 - - + +
434B GLU* 4.1 16.4 - - + +
436B THR* 3.3 18.5 - - + +
441B VAL* 3.4 9.5 - - - +
442B ALA* 2.7 46.8 + - + +
443B VAL 5.0 0.7 - - - -
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Residues in contact with LEU 221 (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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219B PHE* 4.7 0.7 - - + -
220B LEU* 1.3 83.4 - - - +
222B SER* 1.3 56.7 + - - +
234B THR* 3.7 19.5 - - + -
237B GLN* 3.4 39.7 - - + +
238B CYS* 3.9 9.9 - - - +
241B ILE* 3.8 19.7 - - + -
248B ILE* 3.4 30.7 - - + -
249B GLY 2.9 9.4 + - - +
250B VAL* 3.2 11.8 - - + -
251B ALA* 2.7 33.6 + - - +
425B CYS* 3.9 2.7 - - - -
436B THR* 4.2 4.3 - - - -
441B VAL* 4.5 10.1 - - + +
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Residues in contact with SER 222 (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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221B LEU* 1.3 77.6 - - - +
223B MET* 1.3 71.4 - - - +
224B LYS* 3.5 7.4 + - - +
234B THR* 4.2 7.1 + - - +
237B GLN* 5.4 0.7 - - - +
251B ALA* 3.6 11.3 - - - +
424B LYS* 3.4 30.1 - - - +
436B THR* 2.5 38.6 + - - -
437B SER* 4.6 13.8 + - - +
438B LYS* 5.8 0.3 - - - -
440B GLU 5.5 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