Contacts of the strand formed by residues 244 - 249 (chain A) in PDB entry 3QDF
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 THR 244 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A GLU 3.7 0.7 - - - +
192A VAL* 3.3 3.9 - - - +
193A ASN* 2.9 39.4 + - - -
242A GLY 4.6 2.3 + - - -
243A ASP* 1.3 77.0 + - - +
245A VAL* 1.3 63.7 + - - +
246A SER* 4.2 3.3 + - - +
256A THR* 3.5 30.5 - - + -
257A ASN 3.5 11.0 - - - +
258A PRO* 4.4 8.3 - - + +
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Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE* 3.8 15.5 - - + -
116A PHE* 4.0 12.6 - - + -
147A ASN* 3.7 29.7 + - - +
190A THR* 3.8 20.9 - - + -
191A GLU 3.2 9.9 - - - +
192A VAL* 4.3 9.0 - - + -
239A ILE* 4.6 9.4 - - + -
244A THR* 1.3 74.3 - - - +
246A SER* 1.3 63.0 + - - +
247A ILE* 4.5 4.8 - - + +
255A LEU 3.6 1.7 - - - +
256A THR* 3.3 2.3 - - - -
257A ASN* 2.9 40.7 + - + +
259A VAL* 4.3 7.9 - - + -
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Residues in contact with SER 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ARG 3.7 1.0 - - - +
190A THR* 3.3 1.9 - - - -
191A GLU* 2.7 53.0 + - - +
244A THR* 4.2 3.8 + - - +
245A VAL* 1.3 71.2 - - - +
247A ILE* 1.3 60.5 + - - +
248A THR* 4.1 1.5 + - - -
254A THR* 4.0 10.4 - - - +
255A LEU 3.2 4.7 - - - -
256A THR* 2.8 33.0 + - - +
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Residues in contact with ILE 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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116A PHE* 5.9 0.2 - - + -
118A GLY* 3.7 21.3 - - - +
145A ILE* 3.4 27.9 - - + +
146A GLY 3.7 12.6 - - - +
147A ASN* 3.5 43.3 - - + +
188A LEU* 4.3 14.6 - - + -
189A ARG 3.3 4.3 - - - +
190A THR* 3.8 24.5 - - + +
245A VAL* 4.5 3.1 - - + +
246A SER* 1.3 75.3 - - - +
248A THR* 1.3 62.7 + - - +
249A ILE* 4.6 1.8 - - + -
254A THR* 3.2 1.6 - - - -
255A LEU* 2.7 48.9 + - + +
257A ASN* 6.0 0.4 - - - +
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Residues in contact with THR 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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187A GLU 3.8 1.0 - - - +
188A LEU* 3.3 4.3 - - - +
189A ARG* 2.7 77.8 + - - +
191A GLU* 6.1 0.3 - - - -
246A SER* 5.1 1.9 - - - -
247A ILE* 1.3 72.0 - - - +
249A ILE* 1.3 70.3 + - - +
250A GLU* 4.7 2.2 - - - +
253A GLY* 3.2 13.5 - - - +
254A THR* 2.6 27.9 + - - +
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Residues in contact with ILE 249 (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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119A GLU 3.8 5.4 - - - +
120A LEU* 3.6 41.5 - - + +
144A THR 4.2 3.6 - - - +
145A ILE* 3.8 28.8 - - + +
186A LEU* 4.0 15.9 - - + -
187A GLU 3.3 10.3 - - - +
188A LEU* 4.0 18.4 - - + -
202A THR* 5.2 2.2 - - + -
247A ILE* 4.6 0.2 - - + -
248A THR* 1.3 82.6 - - - +
250A GLU* 1.3 76.0 + - - +
251A GLY 3.4 0.2 + - - -
252A ILE* 3.0 32.5 + - + -
253A GLY* 2.9 18.4 + - - +
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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