Contacts of the strand formed by residues 220 - 224 (chain C) in PDB entry 1QK1
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 PHE 220 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C LEU* 5.1 2.5 - - + -
164C LEU* 4.1 13.5 - - + -
187C PHE* 6.0 0.6 - - - -
213C TRP* 3.5 26.3 - + - -
214C HIS* 3.2 8.1 - - - +
215C ASN* 3.1 42.3 + - + +
218C LYS 3.7 0.8 - - - -
219C SER* 1.3 78.9 - - - +
221C LEU* 1.3 59.9 + - - +
222C ILE* 4.2 17.0 - - + -
232C VAL* 3.7 30.1 - - + -
233C ILE 3.4 12.6 - - - -
234C SER* 4.3 9.4 - - - -
247C ARG* 4.2 21.8 - - + -
248C PHE* 4.3 11.2 - + - -
251C GLY* 3.7 33.9 - - - -
252C LEU 4.3 0.7 - - - -
255C VAL* 5.0 4.5 - - + -
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Residues in contact with LEU 221 (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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125C ARG* 6.1 0.2 - - - +
186C HIS 4.8 1.8 - - - +
187C PHE* 3.8 39.0 - - + -
212C ILE* 3.7 14.1 - - + -
213C TRP 3.4 11.7 - - - +
214C HIS* 4.3 4.9 - - + -
220C PHE* 1.3 73.2 - - - +
222C ILE* 1.3 78.0 + - - +
223C TRP* 3.5 40.6 - - + +
231C ARG 3.7 1.1 - - - +
232C VAL* 4.5 0.2 - - - +
233C ILE* 2.8 62.7 + - + +
235C MET* 4.8 10.3 - - + -
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Residues in contact with ILE 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C VAL* 4.9 2.2 - - + -
157C LEU* 3.7 34.1 - - + -
212C ILE* 3.7 1.2 - - - -
213C TRP* 2.8 54.9 + - + +
220C PHE* 4.2 17.7 - - + -
221C LEU* 1.3 82.0 - - - +
223C TRP* 1.3 73.2 + - - +
224C VAL* 4.0 15.7 + - + +
230C THR* 4.5 14.1 - - + -
231C ARG 3.3 6.3 - - - +
232C VAL* 4.2 22.4 - - + -
255C VAL* 4.7 8.1 - - + -
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Residues in contact with TRP 223 (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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125C ARG* 6.3 0.7 - - - -
186C HIS 5.1 2.9 - - - -
187C PHE* 2.9 30.8 + - - -
188C LEU 4.0 7.0 - - - -
189C PHE* 3.4 43.0 - + + -
211C GLY 3.9 1.8 - - - -
212C ILE* 4.2 4.5 - - + -
221C LEU* 3.5 27.3 - - + +
222C ILE* 1.3 79.5 - - - +
224C VAL* 1.3 63.0 + - - +
225C ASN 3.9 0.3 + - - -
226C GLU* 3.6 36.2 + - + -
228C ASP 4.9 0.7 - - - +
230C THR* 3.2 8.3 - - - -
231C ARG* 2.9 48.5 + - + +
233C ILE* 4.8 12.6 - - + -
400C PO4 5.5 7.0 - - - -
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Residues in contact with VAL 224 (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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149C VAL* 4.6 4.3 - - + -
150C GLU* 4.1 20.9 - - + +
153C VAL* 4.1 25.4 - - + -
154C VAL* 5.5 0.9 - - + -
157C LEU* 5.2 1.6 - - + -
168C TYR* 4.1 20.2 - - + +
189C PHE* 4.2 2.3 - - - -
209C ALA 4.2 4.0 - - - +
210C ARG* 3.3 4.7 - - - +
211C GLY 2.9 37.6 + - - +
213C TRP* 5.6 0.2 - - + -
222C ILE* 4.3 12.3 - - + +
223C TRP* 1.3 74.6 - - - +
225C ASN* 1.3 87.5 + - - +
226C GLU 3.4 2.8 + - - -
229C HIS 3.5 8.1 - - - +
230C THR* 4.9 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