Contacts of the helix formed by residues 340 - 351 (chain A) in PDB entry 1GEY
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 THR 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A PRO* 4.1 21.3 - - + +
41A THR* 4.2 11.7 - - - +
275A GLU* 4.1 3.8 - - - -
339A GLY* 1.3 75.2 - - - -
341A ARG* 1.3 65.7 + - - +
342A GLU* 3.5 18.8 - - + +
343A GLU* 3.0 32.7 + - - +
344A SER* 3.0 25.3 + - - -
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Residues in contact with ARG 341 (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 ALA* 4.9 3.2 + - - +
275A GLU* 2.9 45.7 + - - +
278A TYR* 3.5 56.1 - - - +
340A THR* 1.3 74.3 - - - +
342A GLU* 1.3 71.5 + - - +
344A SER 3.4 0.3 + - - -
345A GLN* 3.0 34.9 + - + +
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Residues in contact with GLU 342 (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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340A THR* 3.5 16.7 - - - +
341A ARG* 1.3 98.1 + - - +
343A GLU* 1.3 57.1 + - + +
345A GLN* 3.7 6.0 + - - +
346A ARG* 3.1 28.3 + - - +
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Residues in contact with GLU 343 (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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32A VAL* 4.0 30.4 - - + +
33A TRP 4.9 5.3 + - - +
34A LEU* 3.7 18.8 - - + +
40A PRO* 3.7 14.3 - - - +
339A GLY* 3.2 12.5 - - - +
340A THR* 3.0 38.0 + - - +
342A GLU* 1.3 76.3 - - + +
344A SER* 1.3 64.5 + - - +
346A ARG* 3.3 8.0 + - - +
347A VAL* 3.1 28.5 + - - +
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Residues in contact with SER 344 (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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34A LEU* 5.9 1.1 - - - -
275A GLU* 2.8 33.9 + - - +
278A TYR* 4.6 8.7 - - - -
279A LEU* 3.8 31.5 - - - +
339A GLY 4.8 4.3 + - - -
340A THR 3.0 12.2 + - - -
341A ARG 3.7 2.9 - - - -
343A GLU* 1.3 73.1 - - - +
345A GLN* 1.3 61.5 + - - +
347A VAL* 3.2 6.6 + - - +
348A ILE* 2.9 33.9 + - - +
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Residues in contact with GLN 345 (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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278A TYR* 3.5 17.0 + - - +
341A ARG* 3.0 28.1 + - + +
342A GLU* 3.9 6.5 - - - +
344A SER* 1.3 77.1 - - - +
346A ARG* 1.3 56.7 + - - +
348A ILE* 3.5 28.0 - - + +
349A ASP* 3.0 55.3 + - - +
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Residues in contact with ARG 346 (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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32A VAL* 3.5 27.6 - - + +
317A GLN* 3.0 31.9 + - - +
318A GLY* 4.3 5.1 + - - -
319A ILE* 3.5 18.7 - - + +
342A GLU 3.1 18.5 + - - +
343A GLU* 3.4 11.2 - - - +
344A SER 3.1 0.4 - - - -
345A GLN* 1.3 78.7 - - - +
347A VAL* 1.3 57.2 + - - +
349A ASP* 4.1 5.7 - - - +
350A ALA* 3.2 26.9 + - - +
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Residues in contact with VAL 347 (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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32A VAL* 4.9 0.9 - - + -
34A LEU* 3.5 26.9 - - + -
279A LEU* 5.3 6.7 - - + -
283A LEU* 5.4 2.2 - - + -
314A LEU* 4.7 12.1 - - + -
319A ILE* 3.6 23.3 - - + -
321A LEU* 4.8 2.0 - - + -
336A ILE* 4.6 21.3 - - + -
343A GLU 3.1 15.3 + - - +
344A SER* 3.2 8.5 + - - +
346A ARG* 1.3 74.1 - - - +
348A ILE* 1.3 65.6 + - + +
350A ALA* 3.5 1.7 + - - +
351A LEU* 3.1 41.9 + - + +
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Residues in contact with ILE 348 (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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278A TYR* 3.8 21.8 - - + +
279A LEU* 4.4 13.7 - - + -
282A ALA* 3.6 31.9 - - + +
283A LEU* 5.5 3.8 - - + -
286A ILE* 4.1 20.9 - - + +
344A SER 2.9 21.1 + - - +
345A GLN* 3.5 26.7 - - - +
347A VAL* 1.3 76.5 - - + +
349A ASP* 1.3 66.3 + - - +
351A LEU* 3.1 22.4 + - - +
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Residues in contact with ASP 349 (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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345A GLN* 3.0 44.0 + - - +
346A ARG* 4.1 5.9 - - - +
348A ILE* 1.3 80.4 - - - +
350A ALA* 1.3 61.3 + - - +
351A LEU 3.3 8.1 - - - +
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Residues in contact with ALA 350 (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 SER* 5.4 0.9 + - - -
314A LEU* 3.4 30.4 - - + +
317A GLN* 3.8 23.3 + - - +
319A ILE* 3.5 13.5 - - + -
346A ARG* 3.2 18.7 + - - +
347A VAL 3.8 2.7 - - - +
348A ILE 3.3 0.4 - - - -
349A ASP* 1.3 79.9 - - - +
351A LEU* 1.3 60.2 + - - +
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Residues in contact with LEU 351 (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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283A LEU* 3.5 32.1 - - + -
286A ILE* 3.8 28.1 - - + +
288A CYS* 4.1 14.4 - - - -
289A VAL* 4.5 1.8 - - + -
304A PHE* 4.0 23.1 - - + -
310A VAL* 3.5 32.5 - - + -
314A LEU* 4.3 10.3 - - + -
336A ILE* 5.5 0.4 - - + -
347A VAL* 3.1 33.5 + - + +
348A ILE* 3.1 16.5 + - - +
349A ASP 3.3 9.0 - - - +
350A ALA* 1.3 78.6 - - - +
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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