Contacts of the strand formed by residues 355 - 361 (chain B) 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 ASN 355 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B PRO 4.6 0.8 + - - -
323B LYS 3.8 19.8 + - - +
324B PHE 3.7 4.8 + - - +
325B PRO* 3.6 29.7 - - - +
326B ARG* 2.8 33.4 + - - +
353B GLY 5.2 0.4 - - - +
354B ALA* 1.3 75.2 - - - +
356B ILE* 1.3 57.7 + - - +
357B ASN 5.1 0.2 + - - -
389B THR* 4.9 2.6 + - - -
390B PRO 5.0 6.2 + - - +
391B LYS* 6.3 1.4 - - - +
392B VAL* 3.9 23.0 + - - +
394B CYS* 4.1 2.6 - - - -
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Residues in contact with ILE 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B ARG* 3.4 25.8 - - + +
328B ILE* 4.0 31.4 - - + -
346B VAL* 4.0 23.8 - - + -
349B GLN* 3.8 30.1 - - + -
350B CYS* 4.1 9.6 - - - -
354B ALA* 3.9 10.1 - - + -
355B ASN* 1.3 77.9 + - - +
357B ASN* 1.3 73.5 + - - +
358B PHE* 3.5 5.1 + - + +
392B VAL* 3.9 6.3 - - - +
393B ILE 4.2 0.5 - - - +
394B CYS* 3.5 16.8 - - - +
395B GLY 3.0 25.3 + - - -
396B THR 4.9 0.2 + - - -
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Residues in contact with ASN 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ARG 2.9 12.7 + - - +
327B PHE* 3.4 30.1 - - + -
328B ILE 3.0 24.9 + - - -
355B ASN* 4.2 0.6 + - - -
356B ILE* 1.3 70.2 - - - +
358B PHE* 1.3 62.9 + - - +
380B PHE* 4.5 16.2 - - + -
390B PRO* 5.3 7.5 - - - +
392B VAL* 3.9 32.8 - - + +
398B ILE* 4.8 11.2 - - - +
400B ALA* 5.6 1.2 - - - +
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Residues in contact with PHE 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B ILE* 3.4 22.7 - - + -
330B HIS* 5.1 5.8 - - + -
339B TYR* 3.4 39.3 - + - -
342B ALA* 5.0 2.5 - - + -
343B ALA* 4.2 16.8 - - + -
346B VAL* 3.9 32.1 - - + -
356B ILE* 3.5 8.0 + - + -
357B ASN* 1.3 75.6 + - - +
359B SER* 1.3 60.8 + - - +
360B PRO* 3.2 23.4 - - + +
395B GLY* 3.6 35.2 - - - +
396B THR 3.4 7.8 + - - +
397B PRO* 4.3 5.2 - - + -
398B ILE* 3.1 24.9 + - - +
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Residues in contact with SER 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B PHE* 3.8 26.0 - - - -
328B ILE 2.7 10.3 + - - -
329B TRP* 3.4 7.9 - - - +
330B HIS 3.3 18.0 + - - -
357B ASN* 3.9 0.6 + - - -
358B PHE* 1.3 73.8 - - - +
360B PRO* 1.3 61.4 - - - +
361B TYR* 3.2 19.6 + - - -
398B ILE 3.3 14.6 - - - -
399B PRO* 3.6 0.7 - - - +
400B ALA 2.9 22.9 + - - -
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Residues in contact with PRO 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B HIS 3.5 6.7 - - - +
332B ILE* 3.8 12.9 - - + +
339B TYR* 3.4 32.5 - - + +
358B PHE* 3.2 28.9 - - + +
359B SER* 1.3 85.4 - - - +
361B TYR* 1.3 60.0 + - - +
362B PRO* 3.2 12.6 - - - +
397B PRO* 3.4 32.8 - - + -
398B ILE 3.8 4.3 - - - +
399B PRO* 3.8 10.4 - - - +
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Residues in contact with TYR 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B PHE* 4.9 0.2 - - - -
329B TRP* 3.7 21.7 - + + +
330B HIS 2.9 16.6 + - - +
331B ALA* 3.8 0.2 - - - -
332B ILE* 2.8 27.5 + - - -
333B PRO* 3.4 3.6 - - - +
359B SER* 3.2 30.4 + - - -
360B PRO* 1.3 68.9 - - - +
362B PRO* 1.3 70.0 - - + +
363B ILE 3.3 2.9 + - - +
364B ALA* 3.7 20.1 - - + +
369B ALA* 4.2 12.8 - - + -
372B PHE* 3.2 42.5 + + + -
373B GLY* 3.3 7.1 - - - -
399B PRO* 4.1 12.8 - - + -
400B ALA* 2.8 38.5 + - - +
401B ILE* 4.6 0.2 - - + -
440B PRO* 4.2 13.7 - - + -
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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