Contacts of the strand formed by residues 237 - 248 (chain A) in PDB entry 3DB3
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 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A MSE 3.5 20.0 - - + -
150A ALA* 3.7 17.9 - - + -
151A TRP 5.8 0.2 - - - +
152A PHE* 3.8 28.7 - + + -
191A TYR* 4.5 7.2 - - - -
226A ASN* 3.4 3.1 - - - +
227A TYR 3.0 32.4 + - - +
228A ASN* 6.2 2.9 - - - -
229A PRO* 5.9 2.0 - - + -
236A GLY* 1.3 83.3 - - - -
238A TRP* 1.3 69.8 + + + +
239A TYR* 3.3 17.2 - - + -
8B ARG* 3.7 47.1 - - + -
9B M3L 3.7 18.8 - - + -
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Residues in contact with TRP 238 (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 ALA* 3.2 4.2 - - - +
151A TRP* 2.8 46.3 + - - +
153A GLU* 6.1 1.1 - - - -
224A MSE 4.0 35.4 - - + -
225A LEU* 3.4 23.3 - - - -
226A ASN* 3.4 31.3 - - + +
235A ARG* 3.5 22.0 - - - +
236A GLY 5.0 0.6 + - - -
237A PHE* 1.3 79.7 - + - +
239A TYR* 1.3 61.2 + - - +
276A GLU* 3.1 42.8 - - + -
278A PHE* 3.9 20.9 - + - -
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Residues in contact with TYR 239 (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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148A MSE 3.3 40.3 + - - +
149A GLY 3.7 18.2 - - - -
150A ALA* 3.8 15.3 - - + -
151A TRP* 4.7 0.7 - - - -
223A VAL 3.8 0.2 - - - +
224A MSE 3.3 3.4 - - - -
225A LEU* 2.9 34.9 + - + +
227A TYR* 3.4 34.5 - - + -
229A PRO* 3.9 26.8 - - + +
237A PHE* 3.3 21.5 - - + -
238A TRP* 1.3 72.4 - - - +
240A ASP* 1.3 66.4 + - - +
241A ALA 3.8 0.2 + - - -
259A VAL* 3.6 22.2 - - + -
260A VAL 3.7 12.1 - - - +
261A LEU* 4.0 9.4 - - + -
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Residues in contact with ASP 240 (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 ARG* 4.2 11.2 + - - +
149A GLY 4.9 1.2 + - - -
151A TRP* 3.5 14.7 + - - +
205A ARG* 2.7 45.2 + - - -
222A VAL* 5.0 5.9 - - + +
223A VAL 3.3 3.1 - - - +
224A MSE 3.7 4.3 - - - +
239A TYR* 1.3 77.1 - - - +
241A ALA* 1.3 61.4 + - - +
259A VAL* 3.8 1.0 - - - -
260A VAL* 2.9 41.9 + - + +
280A ILE* 3.5 17.8 - - + +
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Residues in contact with ALA 241 (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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221A GLN 3.6 0.7 - - - +
222A VAL* 3.2 8.2 - - - +
223A VAL* 2.8 34.4 + - - +
225A LEU* 3.9 28.5 - - + -
240A ASP* 1.3 77.9 - - - +
242A GLU* 1.3 59.8 + - - +
257A ALA* 3.9 4.0 - - + -
258A ASN 3.2 13.7 - - - +
259A VAL* 3.7 20.4 - - + -
260A VAL* 4.5 2.9 - - - +
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Residues in contact with GLU 242 (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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220A GLY* 4.3 17.3 - - - +
221A GLN 3.4 4.0 - - - -
222A VAL* 4.1 17.2 - - + +
241A ALA* 1.3 71.9 - - - +
243A ILE* 1.3 74.9 + - - +
244A SER* 3.4 1.4 + - - -
257A ALA* 3.1 4.0 - - - -
258A ASN* 2.8 65.9 + - + +
260A VAL* 5.7 0.4 - - - +
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Residues in contact with ILE 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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217A LEU* 3.6 38.4 - - + -
218A GLU 3.6 20.2 - - - +
219A VAL* 3.6 11.0 - - + +
220A GLY* 2.7 27.0 + - - -
221A GLN* 2.9 34.7 + - + +
223A VAL* 4.1 18.4 - - + -
225A LEU* 5.3 0.4 - - + -
242A GLU* 1.3 75.2 - - - +
244A SER* 1.3 62.5 + - - +
245A ARG 4.4 4.9 - - - +
246A LYS* 5.0 2.5 - - + -
255A LEU* 3.8 29.6 - - + -
256A TYR 3.9 4.5 - - - +
257A ALA* 4.2 5.6 - - + -
277A VAL* 5.1 0.2 - - + -
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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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219A VAL* 3.8 20.5 - - - +
242A GLU 3.9 2.9 - - - -
243A ILE* 1.3 73.8 - - - +
245A ARG* 1.3 72.4 + - - +
256A TYR* 2.9 16.4 + - - -
257A ALA* 3.8 13.2 - - - -
258A ASN* 3.9 23.6 + - - +
268A ASP* 4.6 6.8 + - - +
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Residues in contact with ARG 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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219A VAL* 4.3 4.3 - - - -
243A ILE* 4.8 0.2 - - - -
244A SER* 1.3 87.3 - - - +
246A LYS* 1.3 60.8 + - - +
247A ARG* 3.6 41.1 - - + +
254A GLU 4.4 0.9 - - - -
255A LEU* 3.5 7.2 - - - +
256A TYR* 2.9 67.3 + - + +
268A ASP* 3.4 30.9 + - - -
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Residues in contact with LYS 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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214A TRP* 2.7 66.8 + - + +
215A GLN* 3.5 13.7 + - - +
217A LEU* 3.0 33.1 + - + +
218A GLU* 5.2 1.8 - - - -
219A VAL* 4.3 15.6 - - + +
243A ILE* 5.0 2.0 - - + -
245A ARG* 1.3 75.5 - - - +
247A ARG* 1.3 63.3 + - - +
248A GLU* 4.8 3.5 + - - -
254A GLU 3.4 2.7 - - - -
255A LEU* 4.2 8.7 - - + -
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Residues in contact with ARG 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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214A TRP* 3.6 4.8 - - - -
245A ARG* 3.6 36.2 - - + +
246A LYS* 1.3 82.2 - - - +
248A GLU* 1.3 62.0 + - - +
253A ARG* 3.5 1.7 - - - -
254A GLU* 2.7 75.7 + - + +
256A TYR* 4.6 4.4 + - + -
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Residues in contact with GLU 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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214A TRP* 2.9 36.2 + - + -
246A LYS* 4.8 5.0 - - + -
247A ARG* 1.3 77.0 - - - +
249A THR* 1.3 79.1 + - - +
252A ALA 3.5 10.1 - - - +
253A ARG* 4.3 8.9 - - + +
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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