Contacts of the strand formed by residues 220 - 225 (chain A) in PDB entry 1QQG
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A LYS* 4.5 14.1 - - + -
171A LYS* 3.8 27.8 - - - -
216A HIS* 3.1 10.8 - - - +
217A SER* 2.8 37.8 + - - +
218A GLU* 3.2 16.5 - - - -
219A ASN* 1.3 96.9 - - - +
221A PHE* 1.3 60.9 + - - +
237A TRP* 4.1 20.9 - + + -
238A MET 3.6 6.1 - - - -
239A GLN* 3.1 44.4 - - + -
246A ALA* 3.4 2.9 - - - +
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Residues in contact with PHE 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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185A LEU* 3.8 6.1 - - + -
214A CYS* 3.8 14.1 - - + -
215A GLY 3.1 24.2 - - - -
220A PHE* 1.3 75.8 - - - +
222A PHE* 1.3 68.9 + - - +
223A ILE* 3.5 32.3 - - + -
236A PHE 3.8 0.2 - - - +
237A TRP* 4.7 1.8 - - - -
238A MET* 2.9 53.8 + - + +
240A VAL* 5.1 1.6 - - + -
246A ALA* 4.1 11.0 - - + -
249A MET* 3.8 26.5 - - + -
250A HIS* 3.7 31.2 - - - -
253A ILE* 3.4 31.9 - - + -
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Residues in contact with PHE 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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213A ARG* 4.1 42.4 - - + -
214A CYS* 3.2 33.6 - - - +
215A GLY* 2.9 57.2 + - - -
216A HIS* 3.8 8.1 - - - -
217A SER* 5.8 1.3 - - - -
221A PHE* 1.3 76.7 - - - +
223A ILE* 1.3 69.3 + - - +
224A GLU* 4.4 4.7 - - + -
235A GLU* 4.6 11.4 - - + -
236A PHE 3.2 10.5 - - - +
237A TRP* 3.5 49.6 - + + +
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Residues in contact with ILE 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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185A LEU* 4.3 5.8 - - + -
192A ILE* 3.8 34.3 - - + -
194A PHE* 4.7 4.3 - - + -
206A LEU* 4.8 5.8 - - + -
211A ILE* 3.7 26.9 - - + -
213A ARG 3.7 3.6 - - - -
214A CYS* 4.3 4.0 - - + +
221A PHE* 3.5 28.5 - - + -
222A PHE* 1.3 81.4 - - - +
224A GLU* 1.3 61.7 + - - +
225A VAL* 3.9 17.7 + - + -
234A GLY 3.9 0.3 - - - +
235A GLU* 3.2 3.2 - - - -
236A PHE* 2.9 38.7 + - + +
238A MET* 4.0 12.6 - - + -
253A ILE* 5.2 0.4 - - + -
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Residues in contact with GLU 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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211A ILE* 3.5 3.3 - - - +
212A ARG* 2.8 57.4 + - - -
213A ARG* 2.8 43.0 + - + +
222A PHE* 4.2 4.0 - - + -
223A ILE* 1.3 71.0 - - - +
225A VAL* 1.3 68.1 + - - +
234A GLY* 3.4 13.2 - - - +
235A GLU* 3.8 23.0 - - + +
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Residues in contact with VAL 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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173A LEU* 3.9 7.4 - - + -
206A LEU* 3.8 33.7 - - + -
210A ASN* 3.4 7.9 - - + +
211A ILE* 4.4 9.4 - - + -
212A ARG* 4.0 6.1 - - - +
223A ILE* 4.0 14.1 - - + +
224A GLU* 1.3 83.4 - - - +
226A GLY* 1.3 60.9 + - - +
229A ALA* 3.6 13.9 - - + -
231A THR* 3.8 8.5 - - - +
232A GLY 3.3 23.6 - - - +
233A PRO* 3.7 2.6 - - - +
234A GLY 2.9 31.2 + - - +
236A PHE* 4.7 2.9 - - + -
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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