Contacts of the strand formed by residues 249 - 255 (chain A) in PDB entry 2Q4E
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 MSE 249 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A CYS 3.7 6.3 - - - -
160A PHE* 3.6 22.7 - - + -
247A LEU* 4.4 10.5 - - + -
248A THR* 1.3 82.1 - - - +
250A GLU* 1.3 56.6 + - - +
263A HIS 2.6 32.9 + - - +
264A ASP* 2.7 40.8 - - + +
265A PHE* 4.1 7.0 - - + -
266A ILE* 2.7 40.2 - - + +
267A ILE* 3.3 4.5 - - - +
261B ARG* 5.8 1.0 - - - +
284B PHE* 4.5 7.6 - - - -
291B TRP* 3.1 42.7 - - + +
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Residues in contact with GLU 250 (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 SER* 3.3 7.2 + - - -
159A CYS* 3.0 50.3 + - + +
248A THR* 5.0 3.6 - - + -
249A MSE 1.3 76.0 - - - +
251A ILE* 1.3 77.3 + - - +
252A THR* 4.2 7.6 + - - +
261A ARG* 4.0 7.0 - - - +
262A VAL 3.0 26.9 + - - +
263A HIS* 3.8 23.1 + - - +
265A PHE* 4.0 1.9 - - - -
157B GLN* 5.9 4.9 + - - +
250B GLU* 3.7 22.9 - - - +
252B THR* 4.3 7.3 + - + +
261B ARG* 4.4 13.3 - - - +
263B HIS* 4.1 8.0 - - - -
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Residues in contact with ILE 251 (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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131A TRP* 4.8 7.4 - - + -
140A LEU* 6.2 3.4 - - + -
144A LEU* 6.4 0.2 - - + -
156A VAL* 4.7 8.5 - - + -
157A GLN 3.5 8.5 - - - +
158A SER* 4.6 1.1 - - - +
195A ALA* 3.7 24.0 - - + +
199A ALA* 5.9 2.9 - - + -
250A GLU* 1.3 78.4 - - - +
252A THR* 1.3 68.4 + - - +
253A ALA* 4.6 7.0 - - + +
260A LEU* 3.6 8.2 - - + +
261A ARG* 3.4 7.8 - - - -
262A VAL* 3.1 42.1 + - + -
265A PHE* 3.5 50.5 - - + -
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Residues in contact with THR 252 (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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156A VAL* 2.9 6.4 - - - +
157A GLN* 2.4 77.2 + - + +
250A GLU* 4.2 10.6 + - - +
251A ILE* 1.3 73.9 + - - +
253A ALA* 1.3 60.7 + - - +
254A ILE* 4.0 17.5 - - + -
259A THR* 5.8 0.4 - - + -
260A LEU 3.9 3.6 - - - +
261A ARG* 4.9 7.1 - - + -
157B GLN* 4.6 6.9 + - - +
159B CYS* 5.4 3.1 - - - -
248B THR* 5.3 6.5 - - + -
250B GLU* 3.5 23.0 + - - +
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Residues in contact with ALA 253 (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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144A LEU* 4.6 6.3 - - + -
150A PHE* 4.1 12.2 - - + -
153A LEU* 4.5 7.6 - - + -
155A THR 3.6 4.3 - - - -
156A VAL* 4.1 9.0 - - + +
199A ALA* 4.9 2.7 - - + -
251A ILE* 4.0 4.5 - - + -
252A THR* 1.3 74.6 - - - +
254A ILE* 1.3 62.8 + - - +
255A GLY 3.9 0.8 + - - -
259A THR* 3.5 7.3 - - - +
260A LEU* 3.0 55.1 + - + +
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Residues in contact with ILE 254 (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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150A PHE* 4.3 2.0 - - - -
153A LEU* 3.7 1.0 - - - +
154A LYS* 2.7 34.9 + - + +
155A THR* 2.7 39.6 + - + +
157A GLN* 4.0 8.5 - - - +
252A THR* 4.0 12.3 - - + -
253A ALA* 1.3 74.3 - - - +
255A GLY* 1.3 56.0 + - - +
258A GLY 4.2 1.1 - - - -
259A THR* 4.9 1.1 - - + +
159B CYS* 4.2 14.4 - - - -
161B SER* 3.9 16.2 - - - +
240B TYR* 4.0 18.6 - - + -
245B ALA* 3.6 29.2 - - + -
246B ASN* 4.1 7.6 - - + +
248B THR* 4.7 12.8 - - + +
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Residues in contact with GLY 255 (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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150A PHE* 3.6 21.8 - - - -
152A GLN 3.3 9.6 - - - -
153A LEU* 3.9 2.5 - - - -
154A LYS* 3.9 3.8 - - - -
254A ILE* 1.3 74.8 - - - +
256A THR* 1.3 64.8 + - - -
257A LYS 3.3 2.7 - - - -
258A GLY 2.8 17.8 + - - -
245B ALA* 4.0 1.2 - - - -
246B ASN* 3.1 24.3 + - - +
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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