Contacts of the strand formed by residues 327 - 332 (chain A) in PDB entry 1GQF
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 327 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A THR* 3.6 24.7 - - + -
265A PHE* 3.8 21.8 - - + -
266A ARG 4.6 0.2 - - - -
267A GLY 5.2 1.1 - - - -
278A LYS* 3.5 35.2 - - + -
280A PHE* 3.4 36.3 - + - -
322A PRO 5.7 1.1 - - - -
324A GLU* 3.3 45.7 + - + +
325A ALA 3.1 13.4 - - - -
326A ASP* 1.3 78.1 - - - +
328A LEU* 1.3 56.1 + - - +
329A PHE* 4.1 20.4 - + + -
393A MET* 2.7 39.6 + - + +
394A LEU* 3.2 4.8 - - - +
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Residues in contact with LEU 328 (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 LYS 3.2 7.1 + - - +
279A LEU* 3.8 21.3 - - + -
280A PHE* 3.0 27.0 + - - +
281A PHE* 5.4 4.3 - - + -
327A PHE* 1.3 76.2 - - - +
329A PHE* 1.3 77.1 + - - +
330A ALA* 4.1 3.4 - - + +
366A ILE* 5.0 4.5 - - + -
367A MET* 3.2 31.6 - - + -
370A LEU* 3.6 24.2 - - + -
389A VAL* 3.8 2.7 - - + -
390A VAL 3.3 7.0 - - - +
392A SER* 3.3 23.8 - - - +
394A LEU* 3.5 21.1 - - + -
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Residues in contact with PHE 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ILE* 4.4 8.3 - - + -
262A THR* 3.7 25.1 - - + -
280A PHE* 3.4 27.8 - + + -
282A ILE* 4.2 12.8 - - + -
321A ILE* 3.6 38.8 - - + -
322A PRO 5.2 2.5 - - - -
327A PHE* 4.1 24.7 - + + -
328A LEU* 1.3 80.4 - - - +
330A ALA* 1.3 60.7 + - - +
331A TYR* 3.7 7.6 - + + +
388A CYS 3.5 0.5 - - - +
389A VAL* 3.2 7.1 - - - +
390A VAL* 2.6 54.9 + - + +
393A MET* 4.1 27.1 - - + -
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Residues in contact with ALA 330 (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 PHE 3.0 8.5 + - - -
281A PHE* 4.0 25.4 - - + -
282A ILE* 3.2 23.8 + - - +
328A LEU* 4.5 1.1 - - + -
329A PHE* 1.3 72.9 - - - +
331A TYR* 1.3 61.7 + - - +
349A PHE* 3.5 19.9 - - + -
370A LEU* 4.2 24.9 - - + -
388A CYS 3.4 6.3 - - - -
389A VAL* 4.6 2.9 - - + +
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Residues in contact with TYR 331 (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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238A GLY* 4.5 1.6 - - - -
239A GLU 4.3 13.5 + - - -
241A ASN* 5.6 2.9 + - - -
242A VAL 4.8 4.2 + - - -
258A ILE* 5.0 11.7 - - + +
282A ILE* 3.5 37.2 - - + -
284A ALA* 3.5 26.5 + - + +
329A PHE* 3.7 7.7 - + + +
330A ALA* 1.3 76.0 - - - +
332A SER* 1.3 84.0 + - - +
333A THR* 3.1 26.2 - - + +
349A PHE* 4.6 0.3 - - - -
387A PRO* 3.4 4.3 - - - +
388A CYS* 2.8 46.8 + - + +
390A VAL* 6.0 2.5 - - + -
318B ARG* 4.7 23.6 + - + -
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Residues in contact with SER 332 (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 ILE 3.0 8.3 + - - -
283A GLN* 2.8 26.4 + - - +
284A ALA 3.1 26.2 + - - -
331A TYR* 1.3 81.9 - - - +
333A THR* 1.3 62.3 + - - +
334A VAL* 3.4 17.1 + - - +
349A PHE* 3.5 34.1 - - - +
386A ILE 5.5 0.2 - - - -
387A PRO* 4.6 5.8 - - - -
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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