Contacts of the strand formed by residues 215 - 220 (chain H) in PDB entry 1YEE
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 THR 215 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118H ALA* 3.6 12.5 - - + +
119H PRO* 4.2 20.9 - - + +
208H VAL 5.0 1.1 - - - +
209H ALA* 3.4 3.3 - - - +
210H HIS* 2.9 35.3 + - + +
211H PRO* 5.2 0.3 - - - +
213H SER* 2.6 30.6 + - - -
214H SER* 1.3 76.0 - - - +
216H LYS* 1.3 68.2 + - - +
217H VAL* 4.4 18.2 - - + -
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Residues in contact with LYS 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207H ASN* 3.9 13.3 - - - +
208H VAL 3.4 7.7 + - - +
209H ALA* 3.5 26.7 - - + -
214H SER 4.2 1.2 + - - +
215H THR* 1.3 77.6 - - - +
217H VAL* 1.3 70.6 + - - +
218H ASP* 3.0 34.8 + - - +
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Residues in contact with VAL 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H PRO* 5.5 2.0 - - + +
121H VAL* 3.4 32.3 - - + -
206H CYS 3.9 0.3 - - - +
208H VAL* 2.9 39.1 + - + +
215H THR* 4.4 14.8 - - + -
216H LYS* 1.3 76.6 + - - +
218H ASP* 1.3 76.6 + - - +
219H LYS* 3.9 30.1 - - + +
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Residues in contact with ASP 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204H THR* 3.8 13.2 - - + -
206H CYS 3.4 2.7 - - - -
207H ASN* 2.9 26.8 + - - -
216H LYS* 3.0 25.7 + - - +
217H VAL* 1.3 79.6 - - - +
219H LYS* 1.3 68.6 + - - +
220H LYS 4.1 1.5 + - - -
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Residues in contact with LYS 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H VAL* 3.6 47.1 + - + +
123H PRO* 4.4 20.9 - - + -
140H CYS* 5.2 0.9 - - - -
204H THR* 3.4 3.2 - - - +
206H CYS* 2.8 41.9 + - + +
217H VAL* 3.9 18.9 - - + +
218H ASP* 1.3 74.5 + - - +
220H LYS* 1.3 67.2 + - - +
221H ILE* 3.7 3.3 + - - +
123L GLU* 4.3 24.2 - - - +
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Residues in contact with LYS 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H PRO* 4.0 11.6 - - - +
197H TRP* 5.8 1.0 - - - +
198H PRO 5.8 1.4 + - - -
201H GLN 5.3 2.0 + - - -
202H SER* 4.0 29.4 - - - +
203H ILE 3.6 11.2 - - - +
204H THR* 3.8 14.9 - - + +
218H ASP 4.1 1.2 + - - -
219H LYS* 1.3 77.4 - - - +
221H ILE* 1.3 69.0 + - - +
222H GLU* 3.0 48.1 + - + +
223H PRO* 5.7 1.4 - - - +
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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