Contacts of the strand formed by residues 217 - 220 (chain C) in PDB entry 1XSK
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 SER 217 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 2.6 38.4 + - - +
179C VAL 4.0 0.9 - - - -
180C GLU* 2.9 31.4 + - - -
215C CYS* 4.2 1.5 - - - -
216C VAL* 1.3 71.9 - - - +
218C PHE* 1.3 61.1 + - - +
219C GLU* 4.1 1.6 + - - +
229C GLN* 3.6 1.4 + - - +
230C PHE* 3.3 3.0 - - - -
231C SER* 2.9 43.2 + - - -
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Residues in contact with PHE 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C LEU* 3.8 25.6 - - + -
178C THR* 3.3 10.6 - - - +
179C VAL* 3.0 56.5 + - + +
181C THR* 3.7 15.7 - - + -
198C PRO* 3.9 10.8 - - + -
200C TYR* 4.0 13.5 - + - -
210C VAL* 3.8 24.7 - - + -
216C VAL* 3.1 36.1 - - + -
217C SER* 1.3 74.1 - - - +
219C GLU* 1.3 61.8 + - - +
220C VAL* 3.7 11.7 - - + -
228C VAL* 4.3 15.0 - - + -
229C GLN 3.2 4.3 - - - +
230C PHE* 3.9 13.2 - + + -
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Residues in contact with GLU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 2.7 32.5 + - - +
2C LYS* 3.1 27.2 + - - +
178C THR* 3.2 22.5 + - - +
217C SER 5.0 0.2 - - - +
218C PHE* 1.3 73.1 - - - +
220C VAL* 1.3 59.4 + - - +
221C GLY 2.9 8.7 + - - -
222C SER* 2.6 34.4 + - - +
223C GLU* 4.1 19.1 + - + +
224C LYS 5.0 0.5 + - - +
227C LYS 3.5 1.7 - - - +
228C VAL* 4.7 0.2 - - - -
229C GLN* 2.8 57.2 + - + +
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Residues in contact with VAL 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C LEU* 5.2 1.1 - - + -
162C VAL* 3.7 39.7 - - + -
165C LEU* 4.0 28.0 - - + -
174C ARG* 3.6 20.9 - - + +
175C ASN* 4.0 3.4 - - - +
176C GLY 2.6 32.6 + - - -
177C GLN 3.0 20.8 + - - +
179C VAL* 4.7 1.1 - - + -
218C PHE* 4.1 12.6 - - + -
219C GLU* 1.3 66.1 - - - +
221C GLY* 1.3 53.4 + - - +
222C SER 3.0 3.5 + - - -
227C LYS 4.4 1.6 - - - -
228C VAL* 4.0 16.8 - - + +
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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
------------------------------------------------------------
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