Contacts of the strand formed by residues 264 - 276 (chain A) in PDB entry 4MSL
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 LYS 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A TRP* 4.3 2.0 - - - -
255A ARG* 2.8 56.7 + - - +
263A PHE* 1.3 75.5 - - - +
265A THR* 1.3 67.0 + - - +
266A ILE* 3.2 23.1 + - + +
301A GLY 5.3 0.9 - - - -
302A ASP* 2.8 36.3 + - - +
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Residues in contact with THR 265 (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 GLU* 4.0 15.6 + - - +
253A LEU 3.3 6.7 - - - -
254A TRP* 3.3 48.5 - - + +
263A PHE 5.8 0.7 - - - +
264A LYS* 1.3 77.3 - - - +
266A ILE* 1.3 60.3 + - - +
267A GLY 3.4 5.6 + - - -
268A VAL* 4.8 5.7 - - - +
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Residues in contact with ILE 266 (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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235A PHE* 3.7 36.8 - - + -
253A LEU* 2.6 38.8 + - + +
254A TRP 4.4 0.9 - - - +
255A ARG* 3.8 14.8 - - + +
264A LYS* 3.2 34.0 + - + +
265A THR* 1.3 73.4 - - - +
267A GLY* 1.3 54.4 + - - +
280A LEU* 4.1 2.9 - - + -
300A GLN 3.9 2.5 - - - +
301A GLY* 3.7 34.1 - - - +
304A TRP* 2.7 33.0 + - + -
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Residues in contact with GLY 267 (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 GLU* 3.6 3.6 - - - +
253A LEU* 2.8 34.7 + - - +
265A THR 3.4 2.8 - - - -
266A ILE* 1.3 81.9 + - - +
268A VAL* 1.3 67.8 - - - +
270A ILE* 3.7 15.5 - - - -
304A TRP* 5.0 1.6 - - - -
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Residues in contact with VAL 268 (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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251A LEU 4.0 2.9 - - - -
252A GLU* 3.7 23.8 - - + +
265A THR* 4.8 7.4 - - - +
267A GLY* 1.3 80.9 - - - +
269A LYS* 1.3 78.1 + - + +
270A ILE* 3.1 11.3 + - - +
284A VAL* 3.8 8.7 - - - +
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Residues in contact with LYS 269 (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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249A GLY 2.9 28.8 - - - +
250A ALA* 4.4 12.3 + - + +
251A LEU 3.4 5.1 + - - -
252A GLU* 5.4 0.2 - - - +
268A VAL* 1.3 82.4 - - + +
270A ILE* 1.3 57.5 + - - +
284A VAL* 3.4 14.0 - - + +
285A MET* 3.2 33.5 + - + +
286A ALA 5.5 1.3 - - - -
287A ASP* 3.8 32.0 + - - +
288A LYS 5.6 1.8 - - - +
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Residues in contact with ILE 270 (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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237A THR* 4.0 21.5 - - + -
249A GLY* 3.2 10.0 + - - -
251A LEU* 2.6 53.4 + - + +
253A LEU* 3.6 27.6 - - + +
267A GLY* 3.7 13.9 - - - -
268A VAL 3.5 20.2 - - - +
269A LYS* 1.3 73.2 - - - +
271A TYR* 1.3 62.9 + - - +
272A SER 3.8 21.8 - - - +
273A PHE* 5.1 1.3 - - + -
282A ALA* 4.4 13.9 - - + -
283A SER 3.8 1.6 - - - +
284A VAL* 4.3 17.0 - - + -
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Residues in contact with TYR 271 (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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248A LEU* 3.5 54.1 - - + +
249A GLY 3.9 4.0 - - - +
251A LEU* 4.1 8.6 - - - +
269A LYS 3.7 0.8 + - - -
270A ILE* 1.3 74.5 - - - +
272A SER* 1.3 64.9 + - - +
283A SER* 2.9 20.9 + - - +
284A VAL* 4.8 1.1 - - - +
285A MET* 3.3 31.6 - - + -
292A ARG* 3.4 43.3 + - + -
314A GLN* 4.6 18.0 + - + +
809A 2ET 3.4 23.3 - - - -
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Residues in contact with SER 272 (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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225A LEU* 4.7 9.0 - - - +
237A THR* 5.5 2.0 - - - -
270A ILE* 3.8 8.1 - - - +
271A TYR* 1.3 87.1 - - - +
273A PHE* 1.3 63.4 + - - +
282A ALA* 3.4 2.3 - - - -
283A SER* 2.7 45.2 + - - +
809A 2ET 3.8 26.6 - - - +
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Residues in contact with PHE 273 (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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225A LEU* 3.6 39.9 - - + +
227A LYS* 3.7 38.0 + - + -
235A PHE* 3.7 39.9 - - + -
236A PHE 4.3 0.2 - - - -
237A THR* 3.6 29.2 - - + -
253A LEU* 4.0 16.2 - - + -
270A ILE* 5.1 1.1 - - + -
272A SER* 1.3 77.7 + - - +
274A GLY* 1.3 62.6 + - - +
275A LEU* 4.2 4.9 - - + -
280A LEU* 4.1 15.9 - - + -
281A PHE 3.2 14.8 - - - +
282A ALA* 4.2 8.3 - - + +
809A 2ET 3.7 15.3 - - - +
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Residues in contact with GLY 274 (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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227A LYS* 3.7 12.3 - - - -
273A PHE* 1.3 79.4 - - - +
275A LEU* 1.3 65.5 + - - +
280A LEU* 3.8 1.7 - - - +
281A PHE* 2.9 40.2 + - - +
320A ILE* 5.8 3.4 - - - -
809A 2ET 4.2 11.9 - - - +
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Residues in contact with LEU 275 (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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227A LYS* 3.8 38.6 - - + +
228A TRP 4.8 5.8 - - - +
229A GLY* 4.7 10.5 - - - -
235A PHE* 4.1 28.0 - - + -
273A PHE* 4.2 11.0 - - + -
274A GLY* 1.3 78.6 - - - +
276A GLY* 1.3 60.7 + - - +
277A GLY 5.7 2.5 - - - +
279A PHE 3.7 10.3 - - - +
280A LEU* 4.1 13.7 - - + -
281A PHE* 5.0 1.1 - - - -
320A ILE* 5.4 5.5 - - - +
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Residues in contact with GLY 276 (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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274A GLY 4.2 0.8 + - - -
275A LEU* 1.3 73.8 - - - +
277A GLY* 1.3 69.8 + - - -
279A PHE* 2.8 31.3 + - - +
281A PHE* 4.2 8.5 - - - -
320A ILE* 5.2 3.6 - - - +
323A ALA* 3.5 20.9 - - - -
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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