Contacts of the strand formed by residues 304 - 310 (chain A) in PDB entry 5FHT
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 LEU 304 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A ILE* 5.3 4.5 - - + -
283A ILE* 4.1 16.8 - - + -
294A VAL* 5.0 3.4 - - + -
297A ALA* 3.9 36.6 - - + +
298A VAL* 3.8 23.3 - - + -
301A GLN* 4.0 11.0 - - + +
303A GLN* 1.3 79.7 - - - +
305A ALA* 1.3 59.4 + - - +
306A VAL* 3.6 17.6 + - + +
317A LEU 3.5 1.6 - - - +
318A TYR* 3.3 7.4 - - - +
319A VAL* 2.7 46.6 + - + +
321A PRO* 3.6 29.2 - - + -
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Residues in contact with ALA 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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282A ALA 3.8 0.3 - - - +
283A ILE* 3.4 4.3 - - - +
284A GLY* 2.8 44.7 + - - +
301A GLN* 4.8 1.6 - - - +
303A GLN 4.1 1.2 + - - -
304A LEU* 1.3 69.4 - - - +
306A VAL* 1.3 62.0 + - - +
307A GLN* 3.6 2.1 + - - +
316A THR* 4.2 9.3 - - + +
317A LEU 3.7 3.6 - - - -
318A TYR* 3.6 27.1 - - + -
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Residues in contact with VAL 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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274A LEU* 4.5 8.5 - - + -
280A ILE* 3.8 30.1 - - + -
282A ALA 3.7 4.0 - - - +
283A ILE* 4.7 6.5 - - + +
304A LEU* 3.7 31.6 - - + -
305A ALA* 1.3 71.2 - - - +
307A GLN* 1.3 61.2 + - - +
308A ILE* 3.6 23.8 + - + +
316A THR* 3.4 2.1 - - - -
317A LEU* 2.7 48.9 + - + +
319A VAL* 4.0 16.4 - - + -
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Residues in contact with GLN 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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280A ILE* 3.7 2.8 - - - -
281A LEU* 2.8 51.3 + - + +
282A ALA* 2.9 32.4 + - + +
284A GLY 5.9 0.7 - - - +
287A MET* 5.4 2.6 - - - +
305A ALA 3.6 2.2 + - - +
306A VAL* 1.3 72.9 - - - +
308A ILE* 1.3 57.9 + - - +
314A THR* 3.6 29.1 - - + +
315A LEU 3.3 7.6 - - - +
316A THR* 4.2 13.7 + - + +
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Residues in contact with ILE 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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274A LEU* 3.8 15.0 - - + -
278A ASP* 3.5 31.9 - - + +
279A VAL 3.2 12.6 - - - +
280A ILE* 4.1 7.4 - - + -
281A LEU* 4.2 5.4 - - - -
306A VAL* 3.7 23.1 - - + +
307A GLN* 1.3 78.4 - - - +
309A ARG* 1.3 59.9 + - - +
310A ARG* 3.8 14.8 - - + +
313A GLU 3.9 0.2 - - - +
314A THR* 3.3 7.1 - - - +
315A LEU* 2.8 63.9 + - + +
317A LEU* 4.2 14.6 - - + -
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Residues in contact with ARG 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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252A PRO* 3.7 16.5 - - + +
253A ASP* 3.3 30.3 + - - +
254A VAL* 3.9 19.5 - - + +
277A GLY 4.5 1.2 - - - +
278A ASP* 3.6 4.3 - - - -
279A VAL* 2.8 38.3 + - + +
281A LEU* 3.8 26.5 - - + +
308A ILE* 1.3 73.3 - - - +
310A ARG* 1.3 59.0 + - - +
311A GLY 3.4 21.1 + - - +
312A ARG* 4.1 7.8 - - - +
313A GLU 3.3 18.4 - - - -
314A THR* 3.2 18.3 + - - -
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Residues in contact with ARG 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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273A GLY 3.0 24.0 + - - -
274A LEU* 4.2 0.4 - - - +
275A ARG* 3.3 45.8 - - - +
277A GLY 5.5 1.8 - - - -
278A ASP* 2.8 43.3 + - - +
308A ILE* 3.8 12.9 - - + +
309A ARG* 1.3 73.6 - - - +
311A GLY* 1.3 62.6 + - - +
312A ARG 3.2 0.5 + - - -
313A GLU* 2.8 25.9 + - + +
315A LEU* 3.7 34.7 - - + +
317A LEU* 4.3 3.6 - - - +
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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