Contacts of the strand formed by residues 280 - 289 (chain A) in PDB entry 1EM2
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 GLY 280 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A GLU* 4.0 4.0 - - - -
276A VAL* 2.9 38.6 + - - +
278A PHE 3.3 2.8 + - - -
279A HIS* 1.3 78.5 - - - +
281A LYS* 1.3 66.6 + - - -
282A THR* 3.2 10.6 + - - -
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Residues in contact with LYS 281 (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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260A LYS* 4.1 3.2 - - - +
262A GLU* 5.0 3.2 + - - -
273A THR* 4.0 26.4 + - + +
274A ILE 3.7 2.5 - - - -
275A GLU* 3.1 36.1 + - - +
279A HIS 3.9 1.8 + - - +
280A GLY* 1.3 68.9 - - - -
282A THR* 1.3 61.0 + - - +
283A PHE* 4.0 21.9 + - + -
407A ASN* 3.4 14.4 - - - +
408A THR 5.4 0.3 + - - -
416A ARG* 5.8 8.1 - - - +
420A HIS* 3.5 38.3 + - + +
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Residues in contact with THR 282 (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 ILE* 4.1 8.9 - - + +
273A THR* 3.1 6.4 - - - -
274A ILE* 2.9 43.0 + - + +
276A VAL* 3.5 14.5 - - - +
279A HIS* 5.3 0.2 - - - +
280A GLY 3.2 7.1 + - - -
281A LYS* 1.3 72.4 - - - +
283A PHE* 1.3 67.1 + - - +
284A ILE* 4.7 0.7 - - + -
385A PRO 4.8 1.4 + - - +
405A ILE* 3.4 33.2 - - + -
406A LEU 3.7 12.6 - - - +
407A ASN* 3.1 23.4 + - + +
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Residues in contact with PHE 283 (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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262A GLU* 4.9 4.9 - - + -
271A VAL* 3.9 18.6 - - + -
272A TYR 3.4 2.9 - - - -
273A THR* 3.7 22.0 - - + -
281A LYS* 4.0 22.0 - - + -
282A THR* 1.3 74.3 - - - +
284A ILE* 1.3 62.8 + - - +
285A LEU 4.3 0.2 - - - -
404A TRP 3.6 0.7 - - - +
405A ILE* 3.3 2.9 - - - -
406A LEU* 2.5 48.7 + - - +
420A HIS* 3.6 59.0 - + + -
423A LEU* 4.3 15.7 - - + -
424A ALA* 5.0 5.8 - - + -
427A MSE 3.1 30.5 - - + -
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Residues in contact with ILE 284 (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 ILE* 3.8 8.1 - - + -
259A TRP* 3.6 54.1 - - + +
270A THR 3.5 1.9 - - - +
271A VAL* 3.1 4.9 - - - -
272A TYR* 2.8 47.5 + - + +
273A THR 4.8 0.4 - - - -
274A ILE* 3.7 25.1 - - + -
282A THR* 4.3 6.1 - - + +
283A PHE* 1.3 79.6 - - - +
285A LEU* 1.3 63.7 - - - +
403A VAL* 3.8 27.4 - - + -
404A TRP 3.3 3.8 - - - +
405A ILE* 4.1 11.9 - - + -
427A MSE 4.6 2.2 - - - -
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Residues in contact with LEU 285 (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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269A ASP* 4.1 14.6 - - + -
270A THR 3.4 10.3 - - - +
271A VAL* 4.1 14.6 - - + +
283A PHE 4.3 0.2 - - - -
284A ILE* 1.3 73.1 - - - +
286A LYS* 1.3 60.4 + - - +
287A THR* 3.5 31.4 - - + -
402A PHE* 4.3 11.7 - - + -
403A VAL* 3.2 9.5 - - - +
404A TRP* 2.8 51.6 + - + +
427A MSE 3.6 42.9 - - + +
428A PHE* 4.6 1.1 - - + -
430A PHE* 4.3 8.7 - - + -
431A ALA* 4.2 5.8 - - + -
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Residues in contact with LYS 286 (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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256A GLU* 2.5 31.0 + - - +
259A TRP* 4.2 14.6 - - + -
268A GLY 4.3 1.9 - - - +
269A ASP* 4.0 1.2 - - - -
270A THR* 2.8 38.0 + - - +
272A TYR* 4.1 23.3 + - + +
285A LEU* 1.3 73.0 - - - +
287A THR* 1.3 65.5 + - - +
288A PHE* 4.1 23.6 - - + -
391A LEU* 5.6 4.0 - - - -
401A THR* 3.9 26.9 - - + -
402A PHE 3.4 3.8 - - - +
403A VAL* 4.3 7.6 - - + +
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Residues in contact with THR 287 (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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268A GLY 5.4 1.6 - - - -
269A ASP* 3.1 29.2 - - - +
285A LEU* 3.5 33.4 - - + -
286A LYS* 1.3 79.9 - - - +
288A PHE* 1.3 66.3 + - - +
289A LEU* 4.1 12.2 - - - +
401A THR* 3.7 2.6 - - - -
402A PHE* 2.8 54.8 + - + +
431A ALA* 4.0 6.6 - - + +
434A LEU* 5.0 1.6 - - - +
435A ARG* 4.7 4.0 + - - -
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Residues in contact with PHE 288 (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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268A GLY 5.8 4.0 - - - -
286A LYS* 4.1 23.1 - - + -
287A THR* 1.3 77.5 + - - +
289A LEU* 1.3 66.8 + - - +
290A PRO* 4.2 3.3 - - - +
399A VAL* 5.2 8.3 - - + -
400A CYS 3.6 5.2 - - - +
401A THR* 3.2 35.9 - - + -
435A ARG* 5.7 2.8 + - - -
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Residues in contact with LEU 289 (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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287A THR* 4.1 15.9 - - - +
288A PHE* 1.3 80.9 - - - +
290A PRO* 1.3 66.5 - - + +
291A CYS* 2.9 9.9 + - - -
296A VAL* 3.5 27.8 - - + -
399A VAL* 2.9 19.4 - - - +
400A CYS* 2.9 29.0 + - - +
402A PHE* 3.6 24.2 - - + -
431A ALA 5.8 0.7 - - - +
434A LEU* 3.7 18.2 - - + -
435A ARG* 4.8 18.4 - - + +
438A ILE* 3.7 24.9 - - + -
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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