Contacts of the strand formed by residues 242 - 257 (chain A) in PDB entry 3M8B
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 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A ARG* 6.4 0.9 - - + -
227A THR 3.4 5.6 - - - +
228A ASN* 3.5 17.5 + - - +
241A ASP* 1.3 76.4 + - - +
243A ARG* 1.3 66.2 + - - +
244A LYS* 4.3 3.1 + - + -
275A TYR 4.0 0.3 - - - +
276A ASN* 3.7 4.9 - - - -
277A TYR* 3.3 36.2 + - + +
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Residues in contact with ARG 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLY 4.6 4.0 + - - -
63A LEU* 3.7 29.2 - - - +
95A ASP* 5.2 1.0 + - - -
97A SER* 5.0 2.2 + - - -
98A GLN* 3.5 39.2 - - - +
226A ARG* 3.2 8.1 - - - +
227A THR* 2.7 53.1 + - + +
241A ASP 4.4 0.2 - - - -
242A THR* 1.3 77.2 - - - +
244A LYS* 1.3 67.1 + - - +
245A LEU* 4.1 10.6 - - + +
274A ASP* 3.0 35.0 + - - +
275A TYR 3.4 10.8 - - - +
276A ASN* 4.1 18.1 - - - +
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Residues in contact with LYS 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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224A ASP* 3.7 24.5 + - - +
225A ASN 3.5 11.4 - - - +
226A ARG* 5.3 4.3 - - + -
242A THR* 4.3 3.3 + - + -
243A ARG* 1.3 75.0 - - - +
245A LEU* 1.3 59.5 + - - +
246A TYR* 3.8 25.5 - - - +
273A LYS 3.6 2.1 - - - +
274A ASP* 3.5 3.1 - - - -
275A TYR* 2.8 69.1 + - + -
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Residues in contact with LEU 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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87A LEU* 3.8 32.5 - - + -
98A GLN* 3.4 50.3 - - + +
223A TYR* 3.8 13.6 - - + +
224A ASP* 3.7 1.9 - - - +
225A ASN* 2.9 35.2 + - + +
243A ARG* 4.1 8.4 - - + +
244A LYS* 1.3 75.4 - - - +
246A TYR* 1.3 69.2 + - - +
272A SER* 4.6 4.0 - - - +
273A LYS 3.4 14.6 - - - +
274A ASP* 3.9 26.5 - - + +
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Residues in contact with TYR 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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222A GLY* 4.7 5.3 - - - -
223A TYR* 3.1 33.7 - - - -
224A ASP* 3.9 14.8 - - + -
244A LYS* 3.8 17.4 + - - +
245A LEU* 1.3 76.4 - - - +
247A SER* 1.3 71.8 + - - +
248A GLN* 3.6 37.8 + - + +
271A HIS 5.0 2.5 - - - -
272A SER* 3.1 3.8 - - - -
273A LYS* 2.8 50.1 + - + +
275A TYR* 6.5 0.2 - - + -
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Residues in contact with SER 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASN* 2.7 35.5 + - - -
87A LEU* 4.3 3.6 - - - -
221A TYR* 5.8 1.0 - - - -
222A GLY* 3.0 3.5 - - - -
223A TYR* 3.0 60.3 + - - -
246A TYR* 1.3 84.9 - - - +
248A GLN* 1.3 62.4 + - - +
249A SER* 5.1 0.3 + - - -
271A HIS 3.4 5.4 - - - -
272A SER* 3.5 8.8 - - - -
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Residues in contact with GLN 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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86A ASN* 4.3 0.7 + - - -
221A TYR* 3.1 12.8 - - - +
222A GLY* 4.3 1.8 - - - -
246A TYR* 3.6 29.2 + - + +
247A SER* 1.3 77.4 + - - +
249A SER* 1.3 62.7 + - - +
250A TRP* 4.1 23.9 + - + +
269A TYR* 4.1 10.7 + - + +
270A SER* 3.3 4.2 + - - -
271A HIS* 2.9 62.5 + - + +
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Residues in contact with SER 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASN* 4.1 5.4 + - - -
219A ARG 3.8 0.7 - - - +
220A GLY* 3.5 2.1 - - - -
221A TYR* 2.8 72.7 + - - +
247A SER* 5.1 0.2 + - - -
248A GLN* 1.3 72.6 - - - +
250A TRP* 1.3 68.7 + - - +
251A ASP* 4.9 7.6 - - - -
268A SER* 5.8 1.3 - - - -
269A TYR 3.3 6.1 - - - -
270A SER* 2.9 20.4 + - - -
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Residues in contact with TRP 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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218A VAL* 4.8 14.4 - - + -
219A ARG 3.3 9.4 - - - -
220A GLY* 3.5 31.0 - - - -
221A TYR 5.0 2.0 - - - -
248A GLN* 4.1 28.9 + - + +
249A SER* 1.3 83.1 + - - +
251A ASP* 1.3 62.6 + - - +
267A THR 3.9 0.5 - - - +
268A SER* 3.4 2.3 + - - -
269A TYR* 2.8 60.3 + + + +
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Residues in contact with ASP 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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80A ILE 5.5 0.9 - - - +
81A ASP* 4.6 4.0 - - - +
83A VAL* 4.6 8.3 - - - +
217A PHE* 4.0 10.5 - - + -
218A VAL* 3.5 2.8 - - - +
219A ARG* 2.7 74.5 + - + +
221A TYR* 4.8 10.0 - - - -
249A SER* 4.9 4.6 - - - -
250A TRP* 1.3 76.9 - - - +
252A ALA* 1.3 62.5 + - - +
266A ILE* 4.7 5.6 - - + +
267A THR 3.3 5.3 - - - +
268A SER* 2.9 30.1 + - - -
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Residues in contact with ALA 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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217A PHE* 3.2 16.2 - - - +
218A VAL* 4.3 15.3 - - + -
251A ASP* 1.3 77.3 - - - +
253A GLY* 1.3 59.5 + - - +
266A ILE* 3.5 2.0 - - - +
267A THR* 2.8 43.1 + - - +
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Residues in contact with GLY 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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216A GLY* 3.2 5.4 - - - -
217A PHE* 2.9 55.0 + - - +
252A ALA* 1.3 75.4 - - - +
254A LEU* 1.3 64.2 + - - +
265A LEU 3.1 11.9 - - - -
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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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210A PHE* 4.1 23.6 - - + -
214A TRP* 4.9 19.7 - - + -
215A SER 3.3 14.1 - - - +
216A GLY* 4.4 0.7 - - - -
253A GLY* 1.3 77.2 - - - +
255A ARG* 1.3 64.1 + - - +
263A SER 4.7 0.2 - - - -
264A GLN* 3.5 2.8 - - - -
265A LEU* 2.9 53.0 + - + +
266A ILE* 5.3 0.2 - - - +
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Residues in contact with ARG 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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207A GLU* 6.2 1.4 - - - +
213A ALA 3.6 0.7 - - - +
214A TRP* 3.3 11.5 - - - -
215A SER* 2.7 59.0 + - - +
217A PHE* 3.7 32.7 - - + +
219A ARG* 5.9 0.6 - - - +
254A LEU* 1.3 78.9 - - - +
256A TYR* 1.3 61.3 + - - +
257A ASN* 4.2 4.5 - - + +
263A SER 3.4 6.5 - - - +
264A GLN* 4.5 18.8 - - + -
266A ILE* 5.6 2.2 - - + -
608A MTN 3.7 29.3 + - - +
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Residues in contact with TYR 256 (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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213A ALA* 3.3 30.5 - - + +
214A TRP* 3.7 45.5 - + + -
255A ARG* 1.3 76.1 - - - +
257A ASN* 1.3 59.0 + - - +
258A GLY* 3.4 24.8 - - - -
259A GLU 4.9 0.7 + - - -
261A ILE* 3.4 40.7 - - + +
262A LYS* 3.3 7.4 - - - +
263A SER* 2.8 43.5 + - - +
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Residues in contact with ASN 257 (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 ASP 4.8 1.2 - - - +
213A ALA* 2.8 27.7 + - - +
255A ARG* 5.7 4.3 - - + +
256A TYR* 1.3 74.4 - - - +
258A GLY* 1.3 67.0 + - - +
261A ILE 4.1 1.1 - - - -
262A LYS* 3.9 20.7 - - + -
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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