Contacts of the strand formed by residues 270 - 275 (chain A) in PDB entry 1E1A
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 PRO 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A ALA* 3.7 13.4 - - + +
243A ASN 3.7 13.9 - - - +
244A TRP* 3.3 21.5 + - - +
247A SER* 4.2 3.1 - - - +
248A HIS 3.5 28.0 - - - +
249A ILE* 4.3 6.1 - - + -
265A CYS* 4.2 9.0 - - - -
267A PHE* 3.9 28.2 - - + +
268A GLU 3.2 13.2 - - - +
269A LYS* 1.3 84.5 - - - +
271A SER* 1.3 58.3 + - - +
284A VAL* 4.4 5.2 - - + -
285A THR 3.7 6.5 - - - +
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Residues in contact with SER 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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21A GLU* 3.3 14.9 + - - -
229A ASP* 3.0 26.6 + - - +
230A GLY 2.8 26.3 + - - -
242A ALA* 3.4 4.7 - - - +
244A TRP* 4.2 0.9 - - - -
269A LYS 3.2 0.6 + - - -
270A PRO* 1.3 74.5 - - - +
272A ASN* 1.3 59.3 + - - +
285A THR* 2.7 19.2 + - - -
287A HIS* 3.1 41.6 + - - -
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Residues in contact with ASN 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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21A GLU* 2.7 31.0 - - - +
22A GLY* 4.0 4.9 + - - -
23A PRO* 3.6 19.5 - - + -
74A ALA 4.6 0.2 - - - +
121A ASP* 3.1 24.2 + - - +
230A GLY* 3.3 26.2 - - - -
231A MET 3.9 3.4 + - - +
242A ALA* 4.2 1.8 - - - +
271A SER* 1.3 76.3 - - - +
273A LEU* 1.3 81.8 + - - +
284A VAL* 3.4 5.9 - - - +
285A THR* 2.9 30.7 + - - +
401A CA 4.2 0.5 - - - -
402A CA 4.0 6.1 - - - -
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Residues in contact with LEU 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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23A PRO* 3.5 4.6 - - - +
230A GLY 4.7 5.4 - - - +
231A MET 4.2 0.4 - - - -
232A ASP* 3.1 36.6 - - + +
240A LEU* 4.2 21.3 - - + +
242A ALA* 4.3 13.9 - - + +
249A ILE* 4.0 37.5 - - + -
272A ASN* 1.3 85.2 + - - +
274A HIS* 1.3 57.3 + - - +
275A PHE* 5.2 4.0 - - + -
282A ILE* 3.7 17.9 - - + -
283A PHE 3.0 12.1 - - - +
284A VAL* 4.3 4.5 - - + -
402A CA 2.3 29.5 - - - -
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Residues in contact with HIS 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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23A PRO* 3.2 31.2 + - + +
24A VAL* 3.7 28.3 - - + +
25A PHE* 3.9 14.7 + + + +
31A PHE* 5.2 2.0 - - + -
76A CYS 5.1 0.9 - - - -
77A GLN* 4.3 3.8 - - - -
232A ASP* 3.3 6.4 + - - -
273A LEU* 1.3 75.5 - - - +
275A PHE* 1.3 82.7 + - - +
276A LYS 3.9 0.3 + - - -
281A THR 3.9 0.2 - - - +
282A ILE* 3.5 2.8 - - - +
283A PHE* 2.8 41.0 + - + +
304A GLN* 3.2 44.3 + - + +
306A CYS* 6.1 1.2 - - - -
402A CA 2.6 23.0 - - - -
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Residues in contact with PHE 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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25A PHE* 3.6 5.4 - - - -
232A ASP* 4.6 17.2 + - + -
233A PHE 3.7 21.3 - - - -
234A ASP* 3.8 7.6 - - + -
240A LEU* 4.5 7.0 - - + -
273A LEU* 5.2 2.2 - - + -
274A HIS* 1.3 94.4 - - - +
276A LYS* 1.3 65.3 + - - +
277A PRO* 3.6 4.3 - - + +
279A THR 4.0 7.2 - - - -
280A LYS 4.3 1.3 - - - -
281A THR 3.2 11.0 - - - -
282A ILE* 3.4 38.6 - - + -
297A TRP* 3.7 16.4 - + + -
299A ARG 3.6 15.0 - - - -
301A GLY* 3.4 38.1 - - - +
302A LYS 5.7 2.2 - - - +
304A GLN* 5.9 1.0 - - - +
307A GLU* 5.6 0.9 - - - +
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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