Contacts of the strand formed by residues 214 - 219 (chain X) in PDB entry 3FEW
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 214 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75X GLY 4.5 7.6 - - - +
76X GLN* 3.5 22.6 - - + +
77X VAL 3.2 21.5 + - - -
212X VAL* 3.3 7.5 - - - +
213X ARG* 1.3 80.6 - - + +
215X PHE* 1.3 62.5 + - - +
225X LEU* 3.8 26.7 - - + -
226X VAL 3.6 2.2 - - - -
227X VAL* 4.2 27.7 - - + +
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Residues in contact with PHE 215 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77X VAL* 3.4 39.9 - - + +
79X ILE* 3.9 10.5 - - + -
209X PRO 5.4 2.5 - - - -
212X VAL* 3.4 30.7 - - + -
213X ARG* 3.8 10.5 - - - -
214X LYS* 1.3 75.6 - - - +
216X ASP* 1.3 59.5 + - - +
217X VAL* 3.8 9.2 + - + +
224X TYR 3.1 4.7 - - - +
225X LEU* 3.3 6.7 - - - +
226X VAL* 2.8 47.0 + - + +
228X LEU* 3.6 23.6 - - + -
288X ALA* 3.9 32.8 - - + -
291X VAL* 4.2 14.8 - - + -
292X PHE* 4.3 12.8 - - + -
295X PHE* 5.6 2.5 - + - -
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Residues in contact with ASP 216 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72X ASP* 4.8 4.2 - - - +
76X GLN* 3.8 25.4 - - + +
77X VAL 2.9 11.9 + - - +
78X ARG* 3.5 20.1 + - + +
79X ILE 2.9 24.7 + - - +
214X LYS 4.3 0.6 + - - -
215X PHE* 1.3 69.0 - - - +
217X VAL* 1.3 61.3 + - - +
223X HIS* 2.7 41.9 + - - +
224X TYR 3.5 5.4 - - - +
225X LEU* 4.7 2.5 - - + +
240X THR* 4.6 4.1 + - - -
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Residues in contact with VAL 217 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79X ILE* 3.3 43.7 - - + +
81X ILE* 4.0 22.4 - - + -
215X PHE* 4.0 16.2 - - + +
216X ASP* 1.3 77.2 + - - +
218X ASP* 1.3 62.9 + - - +
219X VAL* 3.7 2.7 + - + -
222X PHE 3.5 1.6 - - - +
223X HIS* 3.3 5.1 - - - -
224X TYR* 2.8 40.7 + - - +
226X VAL* 4.5 1.8 - - + -
284X ALA* 3.9 34.3 - - + +
287X ALA* 4.2 1.6 - - + -
288X ALA* 4.5 1.1 - - + +
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Residues in contact with ASP 218 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79X ILE 2.8 15.3 + - - +
80X THR* 3.9 22.9 + - + +
81X ILE* 3.1 27.4 + - - +
216X ASP 4.1 0.4 + - - -
217X VAL* 1.3 71.3 - - - +
219X VAL* 1.3 60.8 + - - +
220X GLU* 3.7 1.2 + - - -
221X GLN* 2.7 35.2 + - - +
222X PHE 3.2 5.4 - - - -
223X HIS* 4.0 15.4 + - + -
506X NA 2.7 24.6 - - - -
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Residues in contact with VAL 219 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81X ILE* 3.6 29.8 - - + -
217X VAL* 3.7 10.1 + - + -
218X ASP* 1.3 71.9 - - - +
220X GLU* 1.3 77.3 + - + +
222X PHE* 2.8 28.7 + - - +
224X TYR* 4.2 13.7 - - + -
280X ARG* 3.9 33.8 - - + +
283X GLN* 3.8 29.6 - - + +
284X ALA* 4.2 7.9 - - + +
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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