Contacts of the strand formed by residues 304 - 310 (chain A) in PDB entry 2FE5
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 MET 304 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A ASN* 3.8 44.0 - - + +
229A LEU 3.3 8.1 - - - +
230A LEU* 3.9 27.4 - - + +
282A ASN* 4.6 5.9 + - - +
302A SER* 4.4 10.1 + - - -
303A ASP* 1.3 92.4 + - - +
305A VAL* 1.3 61.2 + - - +
306A TYR 4.4 0.3 + - - -
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Residues in contact with VAL 305 (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 VAL 3.5 1.9 - - - +
228A ASN* 3.3 6.0 - - - -
229A LEU 2.8 35.4 + - - +
231A LYS* 4.0 12.3 - - + -
236A LEU* 4.2 15.3 - - + -
281A VAL* 4.0 3.1 - - + -
282A ASN* 4.0 3.1 - - - +
301A THR* 3.4 43.5 - - + +
302A SER 3.5 14.6 - - - +
303A ASP 4.0 5.4 - - - +
304A MET* 1.3 79.1 - - - +
306A TYR* 1.3 63.5 + - - +
307A LEU* 3.7 27.2 + - + +
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Residues in contact with TYR 306 (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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226A GLU* 2.5 52.1 + - + +
227A VAL 3.8 0.7 - - - -
228A ASN* 3.4 30.9 + - - +
280A ALA* 4.8 4.7 - - + -
281A VAL* 3.3 5.4 - - - -
282A ASN* 2.8 67.5 + - - +
304A MET 4.3 0.4 - - - -
305A VAL* 1.3 72.3 - - - +
307A LEU* 1.3 64.3 + - - +
308A LYS* 3.6 34.9 + - + +
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Residues in contact with LEU 307 (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 MET 3.9 0.9 - - - +
226A GLU* 3.4 2.4 - - - -
227A VAL* 2.8 43.6 + - + +
229A LEU* 3.8 33.7 - - + -
236A LEU* 4.9 2.9 - - + -
238A PHE* 3.8 20.2 - - + -
272A LEU* 3.9 9.4 - - + -
278A LEU* 4.2 12.6 - - + -
280A ALA 3.6 2.0 - - - -
281A VAL* 3.8 21.8 - - + -
298A LEU* 3.9 12.3 - - + -
305A VAL* 3.8 22.0 - - + +
306A TYR* 1.3 84.7 - - - +
308A LYS* 1.3 60.7 + - - +
309A VAL* 4.9 5.7 - - + +
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Residues in contact with LYS 308 (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 ILE* 3.6 28.7 - - + -
225A MET 3.4 5.4 - - - +
226A GLU* 4.5 4.9 - - + +
278A LEU* 3.7 1.0 - - - +
279A LEU* 2.8 46.6 + - + -
280A ALA* 3.0 33.0 + - + +
285A ASN* 6.2 0.2 - - - +
306A TYR* 3.6 32.0 + - + +
307A LEU* 1.3 73.0 - - - +
309A VAL* 1.3 58.9 + - - +
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Residues in contact with VAL 309 (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 ILE* 3.3 6.8 - - - +
225A MET* 2.9 47.1 + - + +
227A VAL* 5.2 2.0 - - + -
257A ILE* 4.5 3.6 - - + -
272A LEU* 3.7 28.0 - - + -
276A ASP* 3.9 27.8 - - + +
277A ARG 3.1 12.8 - - - +
278A LEU* 4.0 17.9 - - + -
279A LEU* 4.0 5.4 - - - +
307A LEU* 4.9 2.0 - - + +
308A LYS* 1.3 79.5 - - - +
310A ALA* 1.3 59.0 + - - +
311A LYS* 4.0 15.7 - - + +
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Residues in contact with ALA 310 (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 MET* 3.6 30.7 - - + -
223A THR 3.3 4.5 - - - -
275A GLY 4.6 0.2 - - - +
276A ASP* 3.6 2.8 - - - -
277A ARG* 2.9 55.8 + - + +
279A LEU* 3.8 16.4 - - + +
309A VAL* 1.3 74.4 - - - +
311A LYS* 1.3 64.4 + - - +
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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