Contacts of the strand formed by residues 307 - 315 (chain A) in PDB entry 5E92
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 PHE 307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A LYS* 4.8 7.2 - - + -
294A PHE* 3.6 60.6 - + + +
295A SER* 4.5 10.5 - - - -
300A LYS* 4.4 13.4 + - - +
305A LEU 3.5 2.2 + - - -
306A GLN* 1.3 72.9 + - - +
308A LEU* 1.3 72.5 + - - +
309A THR* 3.5 38.1 - - - -
310A ALA* 3.5 12.1 - - + -
323A LEU* 3.7 21.8 - - + -
324A ILE 4.0 7.9 - - - -
325A THR* 4.3 8.5 - - + -
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 4.7 11.4 - - + -
271A PHE* 6.2 2.2 - - + -
274A VAL* 3.6 31.2 - - + -
306A GLN* 3.7 32.5 - - - +
307A PHE* 1.3 85.5 - - - +
309A THR* 1.4 65.2 + - + +
324A ILE* 2.8 29.0 + - + +
325A THR 4.1 9.9 - - - +
326A ALA* 4.5 4.7 - - + +
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Residues in contact with THR 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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242A LEU* 3.7 30.1 - - + -
307A PHE* 3.5 15.7 - - - -
308A LEU* 1.4 81.4 - - + +
310A ALA* 1.3 68.8 + - - +
311A GLU* 3.8 16.1 - - + +
324A ILE* 2.8 44.6 + - + +
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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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287A TRP* 3.9 10.8 - - + -
291A LYS* 3.7 37.1 - - + -
307A PHE* 3.5 6.8 - - + -
309A THR* 1.3 82.1 + - - +
311A GLU* 1.3 62.9 + - - +
322A TRP 3.3 11.2 - - - +
323A LEU* 3.8 10.8 - - + -
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Residues in contact with GLU 311 (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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240A GLU 4.3 3.0 - - - +
241A LEU* 3.9 18.2 - - + -
242A LEU* 3.1 40.4 + - - +
287A TRP* 4.0 4.5 - - - -
309A THR* 3.8 7.0 - - + +
310A ALA* 1.3 78.0 - - - +
312A GLU* 1.4 64.4 + - - +
313A ARG* 2.8 33.9 + - - +
321A TYR* 3.6 3.1 - - - -
322A TRP* 2.9 43.5 + - + +
324A ILE* 3.6 20.6 - - + +
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Residues in contact with GLU 312 (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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241A LEU* 3.5 20.0 - - - +
284A TYR* 5.1 3.3 + - - -
287A TRP* 4.0 16.6 - - + -
311A GLU* 1.4 74.6 - - - +
313A ARG* 1.3 59.4 + - - +
314A LYS 4.5 0.3 + - - -
319A LYS* 3.3 31.3 + - + +
320A GLN 3.7 5.4 - - - -
321A TYR* 3.7 31.7 + - + -
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Residues in contact with ARG 313 (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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241A LEU* 3.7 27.5 - - + +
242A LEU 2.8 34.2 + - - +
244A ILE* 4.0 13.7 + - - +
311A GLU* 2.8 29.6 + - + -
312A GLU* 1.3 77.8 - - - +
314A LYS* 1.4 65.3 + - - +
315A THR* 3.7 2.4 + - + +
319A LYS* 3.9 4.4 - - - +
320A GLN* 2.8 45.7 + - + +
322A TRP* 3.5 61.2 - - + +
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Residues in contact with LYS 314 (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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241A LEU* 5.8 0.6 - - - +
312A GLU 4.3 0.6 + - - -
313A ARG* 1.4 74.8 - - - +
315A THR* 1.3 71.5 + - - +
316A GLU 5.3 1.4 + - - -
318A GLY* 2.8 34.0 + - - +
319A LYS* 4.3 19.1 - - + +
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Residues in contact with THR 315 (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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313A ARG* 3.7 5.6 + - + +
314A LYS* 1.3 88.6 + - - +
316A GLU* 1.3 63.1 + - - +
317A LEU* 3.9 5.2 + - - +
318A GLY* 3.0 36.4 + - - +
319A LYS* 3.6 3.6 + - - -
320A GLN* 3.7 38.3 - - + +
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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