Contacts of the strand formed by residues 219 - 226 (chain A) in PDB entry 3IQS
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 TYR 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A MET* 4.3 10.8 - - + -
201A THR* 3.6 22.5 - - + +
205A ASN* 3.5 37.5 - - + -
206A PHE* 3.8 25.6 - + + -
217A GLU* 3.8 24.3 + - + -
218A THR* 1.3 76.7 - - - +
220A LEU* 1.3 59.5 + - - +
241A PHE* 4.2 26.7 - + - -
242A LEU 3.4 7.0 - - - -
243A CYS* 3.7 29.0 - - + -
282A PHE 3.7 0.3 - - - +
283A THR* 3.1 5.4 - - - -
284A SER* 2.8 33.2 + - - +
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Residues in contact with LEU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A THR* 5.3 0.4 - - + -
219A TYR* 1.3 76.4 - - - +
221A CYS* 1.3 68.9 + - - +
222A TYR* 3.8 24.2 - - + -
241A PHE* 3.1 3.2 - - - +
242A LEU* 2.8 49.3 + - + +
258A ALA* 4.2 14.4 - - + +
259A GLU* 4.4 13.2 - - + +
262A PHE* 3.8 40.4 - - + -
281A CYS* 4.2 9.9 - - + -
282A PHE 3.2 3.8 - - - -
283A THR* 3.7 24.9 - - + -
295A MET* 4.9 2.9 - - + -
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Residues in contact with CYS 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A MET* 3.8 28.9 - - - -
202A PHE* 6.1 0.7 - - - -
206A PHE* 4.1 16.8 - - - -
220A LEU* 1.3 76.6 - - - +
222A TYR* 1.3 59.8 + - - +
240A GLY 3.4 5.2 - - - -
241A PHE* 3.9 2.9 - - - -
281A CYS* 3.2 4.3 - - - -
282A PHE* 2.7 44.2 + - + +
346A CYS* 4.8 8.1 - - - -
350A PHE* 3.6 39.7 - - + -
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Residues in contact with TYR 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A LEU* 3.8 19.3 - - + -
221A CYS* 1.3 74.7 - - - +
223A GLU* 1.3 68.6 + - - +
224A VAL* 4.6 5.2 - - + -
238A ARG* 5.2 1.3 - - + -
239A ARG* 3.2 14.3 + - - -
240A GLY* 2.8 69.2 + - - +
241A PHE* 3.7 8.9 + - - -
242A LEU* 4.1 17.0 - - + -
262A PHE* 3.7 25.1 - + + -
265A VAL* 4.5 8.0 - - + +
269A TRP* 3.5 39.6 + + + -
279A VAL* 5.1 0.7 - - + -
280A THR 3.1 11.4 - - - +
281A CYS* 4.3 0.9 - - - -
282A PHE* 5.2 0.9 - - - -
350A PHE* 3.5 1.6 - - - -
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Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A TYR* 1.3 81.0 - - - +
224A VAL* 1.3 65.2 + - - +
225A GLU* 4.6 18.4 - - - +
238A ARG 3.5 4.9 - - - +
239A ARG* 3.0 36.9 + - + +
278A ARG 3.6 1.2 - - - +
279A VAL* 3.6 4.5 - - - +
280A THR* 3.0 38.7 + - - +
282A PHE* 3.9 10.2 - - + -
345A HIS* 2.6 38.5 + - - -
349A THR* 3.6 4.7 - - - +
350A PHE* 3.6 16.4 - - + -
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Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A TYR* 4.6 2.7 - - + -
223A GLU* 1.3 77.2 - - - +
225A GLU* 1.3 67.8 + - - +
236A ASN* 4.1 0.3 - - - -
237A GLN* 2.9 32.7 + - + -
238A ARG* 2.9 32.4 + - + +
269A TRP* 3.4 38.6 - - + -
271A LEU* 4.0 13.2 - - + -
277A TYR* 3.9 28.9 - - + -
278A ARG 3.4 6.7 - - - +
279A VAL* 4.5 7.4 - - + -
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Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A GLU* 4.6 19.5 - - + +
224A VAL* 1.3 80.5 - - - +
226A ARG* 1.3 62.2 + - - +
234A LEU* 3.4 38.3 - - + +
235A LEU 3.1 17.5 - - - +
236A ASN* 4.3 15.3 + - - +
237A GLN* 4.0 1.3 - - - -
239A ARG* 5.7 2.1 + - - -
277A TYR* 3.4 2.7 - - - -
278A ARG* 2.6 63.3 + - + +
280A THR* 5.4 2.1 + - - -
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Residues in contact with ARG 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A GLU* 1.3 71.0 - - - +
227A MET* 1.3 67.8 + - - +
228A HIS* 3.4 29.1 + - - +
229A ASN* 4.2 7.1 + - - +
234A LEU* 3.3 6.1 - - - +
235A LEU* 2.9 47.6 + - + +
237A GLN* 3.1 33.2 - - + +
272A ASP* 4.6 7.2 + - - -
275A GLN* 2.9 47.9 - - + +
276A ASP 3.7 5.8 - - - +
277A TYR* 3.7 17.5 - - + -
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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