Contacts of the strand formed by residues 242 - 254 (chain A) in PDB entry 5E6J
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 242 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 3.8 44.9 - - + -
125A GLU 4.8 1.8 - - - +
126A VAL* 3.7 28.0 - - + -
174A LEU* 3.8 30.5 - - + -
179A LEU* 4.3 16.2 - - + -
206A VAL* 3.6 25.6 - - + +
240A SER* 2.8 18.8 + - - -
241A SER* 1.3 89.0 - - - +
243A VAL* 1.3 72.7 + - - +
244A MET* 4.3 11.4 - - + -
260A LEU* 5.5 0.4 - - + -
305A PHE* 4.2 10.8 - + - -
306A TYR 3.3 13.0 - - - +
307A LYS* 4.7 1.6 - - - -
308A GLU* 4.1 2.7 - - - +
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Residues in contact with VAL 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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184A ARG* 3.3 23.8 - - - +
206A VAL 4.0 3.4 - - - +
214A TYR* 3.6 33.2 - - + +
238A GLN* 3.3 26.0 - - + +
240A SER* 3.9 1.1 - - - +
242A PHE* 1.3 88.1 - - - +
244A MET* 1.3 61.8 + - - +
245A MET* 3.6 25.1 - - + -
305A PHE* 3.5 2.8 - - - +
306A TYR* 2.7 43.6 + - + +
308A GLU* 4.4 5.6 - - + -
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Residues in contact with MET 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A VAL* 4.5 1.8 - - + -
167A ARG* 4.1 17.7 - - + -
170A MET* 4.2 14.8 - - + -
174A LEU* 5.8 0.2 - - - -
206A VAL 2.9 20.3 + - - +
207A MET* 3.5 30.4 - - - +
208A TYR 3.1 23.4 + - - -
242A PHE* 4.1 4.4 - - + -
243A VAL* 1.3 73.0 - - - +
245A MET* 1.3 66.9 + - - +
246A SER* 3.6 11.2 + - - +
303A ASP* 3.5 36.8 - - + +
304A VAL 3.8 4.0 - - - +
305A PHE* 3.5 39.7 - - + -
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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
----------------------------------------------------------
208A TYR* 3.7 29.6 - - + -
211A THR* 3.5 24.5 - - + +
212A LEU* 3.2 23.0 - - - +
213A SER 3.4 18.6 - - - +
214A TYR* 4.1 7.2 - - - -
217A LEU* 4.0 23.8 - - + -
243A VAL* 3.6 23.3 - - + -
244A MET* 1.3 73.2 - - - +
246A SER* 1.3 61.5 + - - +
302A THR 4.1 0.3 - - - +
303A ASP* 3.6 0.5 - - - -
304A VAL* 2.8 38.8 + - - +
306A TYR* 3.4 27.1 - - + -
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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
----------------------------------------------------------
167A ARG* 3.4 27.6 - - - +
207A MET* 5.5 0.3 - - - +
208A TYR 2.7 18.7 + - - +
209A MET* 3.6 3.6 - - - -
210A GLY 2.9 21.3 + - - -
211A THR 3.2 8.5 - - - +
212A LEU* 4.3 0.9 - - - -
244A MET* 3.6 13.5 - - - +
245A MET* 1.3 74.9 - - - +
247A ALA* 1.3 64.8 + - - +
302A THR* 3.2 5.4 - - - -
303A ASP* 2.6 27.6 + - - -
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Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A MET* 3.5 11.1 - - - +
210A GLY 3.9 4.9 - - - +
211A THR* 3.9 15.3 - - - +
212A LEU* 3.9 20.0 - - + -
246A SER* 1.3 79.8 - - - +
248A PRO* 1.3 80.8 - - + +
250A ALA* 6.1 0.7 - - + -
302A THR* 2.9 28.4 + - - +
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Residues in contact with PRO 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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209A MET* 3.7 13.9 - - + -
210A GLY* 5.1 6.7 - - - +
212A LEU* 5.6 0.2 - - - +
247A ALA* 1.3 94.1 - - + +
249A PRO* 1.3 78.4 - - + +
250A ALA* 3.0 12.1 + - - +
269A TYR* 3.8 13.0 - - - +
301A VAL 4.2 1.4 - - - +
8B LEU* 5.0 7.6 - - + -
70B VAL* 4.2 23.8 - - + -
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Residues in contact with PRO 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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247A ALA 3.5 3.3 - - - +
248A PRO* 1.3 81.3 - - + +
250A ALA* 1.3 60.6 + - - +
265A TYR* 3.8 34.5 - - + +
267A GLY 6.0 1.3 - - - +
269A TYR* 3.7 20.2 - - + +
300A PRO* 4.6 9.2 - - + +
301A VAL 3.8 10.8 - - - +
302A THR* 4.5 1.6 - - - -
73B LEU* 3.6 33.0 - - + -
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Residues in contact with ALA 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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212A LEU* 5.1 7.6 - - + -
247A ALA* 6.1 0.2 - - + -
248A PRO 3.0 11.2 + - - +
249A PRO* 1.3 74.8 - - - +
251A GLU* 1.3 67.4 + - - +
252A TYR* 3.3 4.0 + - - +
299A GLY 3.1 0.2 - - - +
300A PRO* 3.6 7.2 - - - -
301A VAL* 2.8 34.9 + - - +
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Residues in contact with GLU 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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250A ALA* 1.3 75.6 - - - +
252A TYR* 1.3 62.6 + - - +
298A LYS* 4.1 4.0 - - - +
299A GLY* 3.2 26.5 + - - -
300A PRO* 3.7 22.4 - - - +
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Residues in contact with TYR 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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212A LEU* 3.5 35.4 - - + -
213A SER* 3.8 27.5 - - - -
250A ALA 4.0 0.2 - - - +
251A GLU* 1.3 76.6 - - - +
253A LYS* 1.3 74.4 + - - +
254A LEU* 3.5 26.0 - - + +
259A PHE* 6.5 0.4 - + - -
297A TYR 3.2 12.5 - - - +
298A LYS* 4.4 2.2 - - - -
299A GLY 2.8 24.4 + - - +
301A VAL* 3.4 19.7 - - + -
304A VAL* 4.9 8.3 - - + -
306A TYR* 4.3 6.4 + - - -
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Residues in contact with LYS 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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252A TYR* 1.3 88.7 - - - +
254A LEU* 1.3 65.8 + - - +
255A GLN* 3.9 14.6 + - + +
296A GLU* 5.4 6.5 - - + +
297A TYR 3.4 5.8 - - - +
298A LYS* 4.5 8.3 - - + +
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Residues in contact with LEU 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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252A TYR* 3.5 36.3 - - + +
253A LYS* 1.3 73.1 - - - +
255A GLN* 1.3 60.9 + - - +
259A PHE* 3.6 34.3 - - + -
262A ALA* 3.8 17.9 - - + -
277A ILE* 3.7 26.0 - - + -
283A LEU* 4.1 8.3 - - + +
296A GLU* 3.6 26.7 - - - +
297A TYR* 2.8 24.1 + - + +
301A VAL* 3.8 22.2 - - + -
304A VAL* 5.4 2.5 - - + -
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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