Contacts of the strand formed by residues 244 - 255 (chain B) 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 LEU 244 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A LYS* 3.9 22.2 + - - +
256A THR* 4.5 6.3 + - - -
162B PHE 4.0 0.2 - - - -
163B ALA* 4.9 2.5 - - - +
164B GLY 4.9 3.1 - - - +
169B LEU* 3.7 29.8 - - + -
215B VAL* 5.6 5.4 - - + -
223B LEU* 3.2 58.8 - - + +
224B SER* 4.1 6.7 - - - +
242B SER* 3.1 8.1 + - - +
243B PHE* 1.3 84.0 - - - +
245B ALA* 1.3 61.6 + - - +
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Residues in contact with ALA 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LYS* 3.7 16.8 - - + -
254A ILE* 3.6 23.1 - - + -
255A GLY 4.0 3.6 - - - -
256A THR* 4.8 2.9 - - - +
161B SER* 3.3 1.4 - - - -
162B PHE 2.7 29.2 + - - -
163B ALA* 3.9 1.5 - - - +
240B TYR* 4.9 1.3 - - - +
242B SER* 3.2 24.0 + - - +
244B LEU* 1.3 76.5 - - - +
246B ASN* 1.3 71.4 + - - +
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Residues in contact with ASN 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A ILE* 4.1 1.6 - - + +
255A GLY 3.1 21.6 + - - +
256A THR 3.8 6.9 + - - +
257A LYS* 2.7 31.7 - - - +
258A GLY 3.6 9.0 - - - +
259A THR* 3.0 25.1 + - - +
279A SER* 3.7 19.0 + - - -
280A THR* 4.6 0.2 - - - +
281A LYS* 3.9 8.5 + - - -
282A ALA* 4.5 8.1 + - - +
161B SER* 2.8 12.5 + - - -
162B PHE* 3.5 0.2 - - - -
163B ALA* 4.0 12.5 - - - +
245B ALA* 1.3 78.6 - - - +
247B LEU* 1.3 80.7 + - - +
248B THR* 3.3 3.6 + - - -
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Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A THR* 3.3 6.9 + - - -
279A SER* 4.6 4.2 + - - -
282A ALA* 3.7 18.1 + - + +
283A TRP* 3.8 31.2 - - + +
284A PHE* 3.7 23.8 - - + -
291A TRP* 3.7 35.3 - - + -
160B PHE* 4.0 3.6 - - + -
161B SER 3.0 21.8 - - - +
162B PHE* 3.3 21.0 - - + +
163B ALA* 3.9 2.4 - - - +
246B ASN* 1.3 79.4 + - - +
248B THR* 1.3 67.2 + - - +
249B MSE 3.4 24.9 - - + -
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Residues in contact with THR 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A THR* 5.3 2.7 - - + -
254A ILE* 4.7 11.7 - - + +
259A THR* 2.6 47.4 + - + +
261A ARG* 4.3 18.4 - - - +
291A TRP* 4.9 4.5 - - - -
159B CYS* 3.9 14.7 - - - +
160B PHE* 3.4 4.0 - - - -
161B SER* 3.0 39.6 + - - +
246B ASN 3.2 3.3 + - - -
247B LEU* 1.3 76.8 + - - +
249B MSE 1.3 67.7 + - - +
250B GLU* 5.0 5.2 - - - +
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Residues in contact with MSE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A ARG* 5.3 1.4 + - - -
284A PHE* 3.7 16.2 - - + -
291A TRP* 3.3 29.9 - - + -
159B CYS 3.6 8.5 - - - +
160B PHE* 4.1 18.8 - - + -
247B LEU* 3.4 26.9 - - + -
248B THR* 1.3 78.5 - - - +
250B GLU* 1.3 67.6 + - - +
263B HIS* 2.8 36.6 + - - +
264B ASP* 3.7 12.3 - - - -
265B PHE* 4.3 1.8 - - + +
266B ILE* 4.0 15.3 - - + -
267B ILE* 3.5 30.7 - - + +
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Residues in contact with GLU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A GLU* 3.7 5.6 - - - +
252A THR* 3.5 25.9 + - - +
261A ARG* 4.1 10.0 - - - -
157B GLN* 4.7 13.0 - - - +
158B SER* 2.8 30.5 + - - -
159B CYS* 3.6 19.5 + - - +
248B THR* 5.0 4.0 - - + +
249B MSE 1.3 79.5 - - - +
251B ILE* 1.3 54.4 + - - +
252B THR* 2.8 26.3 + - - +
262B VAL 2.8 17.0 - - - +
263B HIS* 3.5 28.3 + - - +
265B PHE* 3.4 14.3 - - - -
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Residues in contact with ILE 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B TRP* 4.2 12.6 - - + -
140B LEU* 4.5 7.4 - - + -
144B LEU* 6.3 0.4 - - + -
156B VAL* 3.8 26.0 - - + +
157B GLN 3.8 4.9 - - - +
158B SER* 4.1 3.4 - - - +
195B ALA* 4.0 18.4 - - + +
250B GLU* 1.3 74.9 - - - +
252B THR* 1.3 70.3 + - - +
253B ALA* 4.0 4.7 - - + +
260B LEU* 3.5 10.4 - - + +
261B ARG* 3.4 6.6 - - - +
262B VAL* 2.7 40.9 + - + +
265B PHE* 3.3 47.6 - - + -
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Residues in contact with THR 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A CYS* 5.2 5.6 - - + -
248A THR* 4.7 7.6 - - + -
250A GLU* 4.3 6.5 + - + +
155B THR* 3.7 4.1 - - + +
156B VAL* 3.1 18.6 + - - -
157B GLN* 3.0 40.6 + - + +
250B GLU* 2.8 28.2 + - - -
251B ILE* 1.3 72.4 + - - +
253B ALA* 1.3 58.5 + - - +
254B ILE* 4.3 21.1 - - + -
259B THR* 5.3 0.7 - - + -
260B LEU 3.4 7.0 - - - +
261B ARG* 3.8 16.6 - - + +
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Residues in contact with ALA 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B LEU* 3.8 27.6 - - + -
150B PHE* 4.5 1.1 - - - -
153B LEU* 4.3 4.0 - - + -
155B THR 3.0 7.2 - - - +
156B VAL* 3.3 24.5 - - + +
251B ILE* 4.0 1.2 - - + +
252B THR* 1.3 72.6 - - - +
254B ILE* 1.3 69.1 + - - +
259B THR* 3.2 0.9 - - - +
260B LEU* 2.6 45.8 + - + +
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Residues in contact with ILE 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A CYS* 4.7 8.1 - - + -
160A PHE 6.1 0.4 - - - +
161A SER* 4.6 7.4 - - - +
240A TYR* 5.4 2.0 - - + -
245A ALA* 3.9 6.5 - - + -
246A ASN 3.3 33.4 - - - +
248A THR* 3.4 33.7 - - + +
150B PHE* 3.5 5.8 - - - -
154B LYS* 3.1 26.3 + - - +
155B THR* 2.7 38.0 + - + -
252B THR* 4.3 10.8 - - + -
253B ALA* 1.3 82.0 - - - +
255B GLY* 1.3 62.9 + - - +
258B GLY 3.3 4.7 - - - +
259B THR* 3.3 16.8 - - + +
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Residues in contact with GLY 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ALA* 4.2 3.8 - - - -
246A ASN* 2.7 36.5 + - - +
150B PHE* 3.1 17.4 - - - -
152B GLN 3.2 16.6 - - - -
154B LYS* 4.4 1.3 - - - -
254B ILE* 1.3 73.7 - - - +
256B THR* 1.3 58.3 + - - -
257B LYS 3.1 3.8 - - - -
258B GLY 2.5 12.4 + - - -
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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