Contacts of the strand formed by residues 325 - 331 (chain A) in PDB entry 3GUU
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 PRO 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A VAL* 3.4 21.5 - - - +
208A GLY* 3.3 23.7 - - - -
209A ALA 3.3 3.5 + - - -
323A LYS 3.9 0.6 - - - +
324A PHE* 1.4 85.1 - - + +
326A ARG* 1.3 59.4 + - - +
355A ASN* 3.5 25.6 - - - +
380A PHE* 3.4 16.4 - - + -
384A ALA* 5.4 0.4 - - + -
389A THR* 3.3 31.6 - - + +
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Residues in contact with ARG 326 (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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191A VAL* 4.9 1.4 - - - +
194A THR* 4.4 7.9 + - + -
209A ALA* 3.3 15.0 - - + +
211A HIS* 5.2 5.4 + - - +
322A PRO* 3.0 39.4 + - - +
324A PHE* 3.5 36.5 - - + -
325A PRO* 1.3 77.5 - - - +
327A PHE* 1.3 53.8 + - - +
328A ILE* 4.2 13.3 - - + +
345A TYR* 2.5 42.2 + - - -
349A GLN* 3.1 16.3 + - - -
354A ALA* 3.6 13.9 - - - +
355A ASN 2.8 10.1 + - - +
356A ILE* 3.8 21.3 - - + +
357A ASN* 2.8 32.4 + - - +
380A PHE* 3.4 11.2 - - - -
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Residues in contact with PHE 327 (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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209A ALA 3.0 6.9 + - - +
210A SER* 3.2 25.5 - - - +
211A HIS 3.1 23.6 + - - -
326A ARG* 1.3 72.3 - - - +
328A ILE* 1.3 63.5 + - - +
329A TRP* 3.3 31.4 - + + -
357A ASN* 3.3 31.2 - - - -
359A SER* 3.6 33.4 - - - -
361A TYR* 4.8 1.3 - - - -
373A GLY 3.9 3.1 - - - -
376A PRO* 3.7 19.3 - - + -
377A SER* 3.8 20.4 - - - -
380A PHE* 3.5 26.2 - + + -
400A ALA* 3.8 12.3 - - + -
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Residues in contact with ILE 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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211A HIS* 3.1 41.1 - - + +
214A THR* 4.4 8.3 - - - +
326A ARG* 4.6 9.0 - - + +
327A PHE* 1.3 83.0 - - - +
329A TRP* 1.3 60.7 + - - +
330A HIS* 6.0 1.1 - - + -
342A ALA* 5.6 6.7 - - + -
345A TYR* 4.2 13.2 - - + -
346A VAL* 4.1 22.4 - - + -
356A ILE* 4.0 35.7 - - + -
357A ASN 3.0 6.9 + - - +
358A PHE* 3.3 13.9 - - + -
359A SER 2.8 30.0 + - - -
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Residues in contact with TRP 329 (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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181A GLU* 3.5 22.2 - - - -
182A GLY 4.2 4.5 - - - -
183A TYR* 3.4 33.4 - + + -
210A SER 4.1 0.7 - - - -
211A HIS 3.0 42.1 + - - +
212A GLY* 3.0 11.4 - - - -
213A GLY 3.0 21.0 + - - -
214A THR 4.6 0.2 + - - -
327A PHE* 3.3 27.4 - + + -
328A ILE* 1.3 78.4 - - - +
330A HIS* 1.3 65.1 + - - +
358A PHE* 5.2 0.7 - - - -
359A SER* 3.2 21.8 - - - +
361A TYR* 3.7 15.5 - + + -
369A ALA* 2.7 32.8 + - + -
370A GLU 4.4 6.7 - - - -
373A GLY* 3.6 23.0 - - - -
374A LEU* 4.6 1.6 - - - -
377A SER* 3.6 21.1 - - - -
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Residues in contact with HIS 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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183A TYR* 5.7 0.2 - - - -
213A GLY* 3.6 9.9 - - - +
214A THR* 3.4 33.0 + - - -
328A ILE* 6.0 0.9 - - + -
329A TRP* 1.3 76.0 - - - +
331A ALA* 1.3 79.7 + - - +
334A ASP* 3.1 16.6 - - + -
337A VAL* 2.9 36.4 + - - +
338A PRO 3.7 5.1 + - - -
339A TYR* 3.7 30.0 - + + -
342A ALA* 3.8 18.6 - - + -
358A PHE* 5.0 6.7 - - + -
359A SER 3.1 7.1 + - - +
360A PRO* 3.3 4.0 - - + +
361A TYR* 2.8 29.0 + - - -
369A ALA* 4.5 0.9 - - - -
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Residues in contact with ALA 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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183A TYR* 5.2 0.4 + - - -
330A HIS* 1.3 87.4 + - - +
332A ILE* 1.3 65.4 + - - +
334A ASP* 3.1 21.2 + - + +
339A TYR* 3.6 1.8 - - - +
361A TYR* 3.8 6.1 - - - -
364A ALA* 3.6 20.9 - - + -
365A GLU 3.3 36.1 - - - +
366A HIS 4.3 0.2 - - - +
369A ALA* 3.7 12.7 - - + +
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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