Contacts of the strand formed by residues 242 - 248 (chain A) in PDB entry 2QQM
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 ILE 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A ILE* 3.7 24.7 - - + -
177A VAL 3.4 4.3 - - - +
178A PHE* 3.8 24.0 - - + -
185A ILE* 3.9 0.7 - - - -
216A GLY* 3.1 36.7 + - - -
217A PHE* 3.6 35.4 - - + +
238A SER* 3.0 11.4 + - - -
240A SER* 2.8 18.6 + - - +
241A GLY* 1.3 82.6 - - - +
243A LEU* 1.3 61.3 + - - +
244A SER* 3.7 1.3 - - - +
439A SER* 3.9 12.8 - - - +
441A LEU* 3.9 17.3 - - + -
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Residues in contact with LEU 243 (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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158A ILE* 5.3 1.1 - - + -
175A TYR 4.0 0.6 - - - +
176A ILE* 3.4 1.9 - - - +
177A VAL* 2.8 47.7 + - + +
185A ILE* 3.6 25.9 - - + +
187A LEU* 4.2 25.4 - - + -
213A ILE* 4.3 3.4 - - + -
214A TRP 3.7 9.2 - - - +
224A ILE* 4.8 0.4 - - + -
236A ILE* 3.6 29.8 - - + -
238A SER* 3.7 20.6 - - - +
242A ILE* 1.3 72.4 - - - +
244A SER* 1.3 66.3 + - - +
245A MET* 3.9 25.4 - - + -
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Residues in contact with SER 244 (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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174A THR* 5.3 0.2 - - - -
175A TYR 3.1 9.4 - - - -
176A ILE* 3.6 18.5 - - - +
213A ILE* 3.4 1.4 - - - +
214A TRP* 2.8 39.6 + - - +
216A GLY 2.6 28.0 + - - -
217A PHE* 3.6 5.2 - - - -
218A PRO* 3.7 23.6 - - - +
243A LEU* 1.3 73.9 - - - +
245A MET* 1.3 69.7 + - - +
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Residues in contact with MET 245 (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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158A ILE* 3.8 39.7 - - + -
173A CYS 3.8 0.3 - - - +
174A THR* 3.9 1.0 - - - +
175A TYR* 2.8 46.5 + - + +
187A LEU* 3.7 22.7 - - + -
189A PHE* 3.9 2.7 - - + -
211A LEU* 3.9 17.9 - - + -
212A GLU 3.0 9.0 - - - +
213A ILE* 3.8 30.5 - - + -
214A TRP* 4.6 0.7 - - - -
243A LEU* 3.9 6.7 - - + -
244A SER* 1.3 80.4 - - - +
246A VAL* 1.3 67.6 + - - +
247A PHE 4.3 0.2 - - - -
258A PHE* 4.2 14.4 - - + -
260A ALA* 6.0 0.2 - - + -
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Residues in contact with VAL 246 (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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172A GLU* 3.9 16.6 - - + +
173A CYS 3.3 8.3 - - - +
174A THR* 3.8 18.2 - - - +
210A ARG 3.7 1.6 - - - +
211A LEU* 3.5 3.7 - - - -
212A GLU 2.8 36.9 + - - -
214A TRP* 3.7 19.9 - - + -
218A PRO* 3.9 18.4 - - + -
245A MET* 1.3 79.1 - - - +
247A PHE* 1.3 63.1 + - - +
248A TYR* 3.4 42.9 - - + +
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Residues in contact with PHE 247 (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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160A SER* 4.0 18.2 - - - -
161A PRO* 4.0 8.5 - - + -
167A TYR* 3.7 23.3 - + - -
171A LEU* 3.6 25.0 - - + +
172A GLU* 3.2 6.8 + - - -
173A CYS* 2.9 34.6 + - + +
175A TYR* 3.9 15.0 - - + -
194A LEU* 3.3 33.2 - - + -
210A ARG 3.4 13.9 - - - -
211A LEU* 3.6 14.3 - - + +
245A MET 4.3 0.2 - - - -
246A VAL* 1.3 72.4 - - - +
248A TYR* 1.3 59.0 + - - +
249A THR* 3.2 29.8 - - + -
258A PHE* 3.9 15.0 - + - -
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Residues in contact with TYR 248 (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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171A LEU 3.4 5.8 - - - +
172A GLU* 3.7 38.0 + - + -
208A TYR 4.8 1.6 - - - +
209A ASP* 3.2 2.9 - - - -
210A ARG* 2.8 90.2 + - + +
212A GLU* 3.7 18.6 - - + -
214A TRP* 4.7 6.9 - - - -
219A ASP* 5.4 3.3 + - - -
246A VAL* 3.4 32.1 - - + +
247A PHE* 1.3 72.0 - - - +
249A THR* 1.3 67.7 + - - +
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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