Contacts of the strand formed by residues 213 - 218 (chain C) in PDB entry 4YHP
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 213 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126C GLY* 4.1 6.2 - - - -
127C PRO* 4.0 23.3 - - + +
206C VAL 3.9 0.9 - - - +
207C ASN* 3.6 1.8 + - - +
208C HIS* 2.7 38.9 + - - +
211C SER* 2.9 31.0 + - - -
212C ASN* 1.3 74.3 + - - +
214C LYS* 1.3 64.2 + - - +
215C VAL* 4.1 20.9 - - + -
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Residues in contact with LYS 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C VAL 3.4 4.5 - - - +
207C ASN* 3.3 31.2 - - + +
209C LYS* 5.8 3.8 - - - +
212C ASN 4.2 2.1 + - - -
213C THR* 1.3 74.3 - - - +
215C VAL* 1.3 69.5 + - - +
216C ASP* 6.1 2.0 - - - +
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Residues in contact with VAL 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C PRO* 4.6 7.9 - - + +
129C VAL* 3.6 38.6 - - + +
204C CYS 3.6 2.4 - - - +
205C ASN* 3.7 1.2 - - - -
206C VAL* 2.7 43.3 + - + +
213C THR* 4.1 17.9 - - + -
214C LYS* 1.3 80.7 - - - +
216C ASP* 1.3 75.4 + - - +
217C LYS* 4.5 3.6 - - + -
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Residues in contact with ASP 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C ILE* 3.9 12.3 - - + -
204C CYS 3.5 2.0 - - - -
205C ASN* 2.6 37.5 + - - +
214C LYS* 6.1 1.9 - - - +
215C VAL* 1.3 79.5 - - - +
217C LYS* 1.3 63.1 + - - +
218C LYS 4.4 0.3 + - - -
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Residues in contact with LYS 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C VAL* 3.7 31.3 + - + +
131C PRO* 3.6 34.8 - - - +
148C CYS* 4.3 8.1 - - - -
203C ILE* 3.3 5.6 - - - +
204C CYS* 3.0 43.9 + - - -
215C VAL* 4.5 4.7 - - + -
216C ASP* 1.3 75.6 - - - +
218C LYS* 1.3 74.8 + - - +
219C VAL* 3.5 6.6 + - + +
124D SER* 4.8 9.3 + - - -
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Residues in contact with LYS 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C PRO* 4.7 1.7 - - - +
201C THR* 4.2 32.9 + - + +
202C TYR 3.5 10.3 - - - +
203C ILE* 4.0 11.8 - - + +
216C ASP 4.3 0.2 - - - -
217C LYS* 1.3 89.7 + - - +
219C VAL* 1.3 63.3 + - - +
220C GLU* 3.3 44.4 + - + +
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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