Contacts of the strand formed by residues 325 - 331 (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 PRO 325 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B VAL* 3.5 16.2 - - - +
208B GLY* 3.2 25.5 - - - -
209B ALA 3.3 2.8 + - - -
323B LYS 4.6 0.2 - - - +
324B PHE* 1.3 89.0 - - + +
326B ARG* 1.3 59.3 + - - +
355B ASN* 3.6 24.7 - - - +
380B PHE* 3.6 16.3 - - + -
384B ALA* 5.5 0.4 - - + -
389B THR* 3.5 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B VAL* 4.9 1.8 - - - +
194B THR* 4.5 6.7 + - - -
209B ALA* 3.1 17.0 - - + +
211B HIS* 5.0 5.1 + - - -
322B PRO* 3.2 41.4 + - - +
324B PHE* 3.7 27.7 + - + +
325B PRO* 1.3 79.8 - - - +
327B PHE* 1.3 59.9 + - - +
328B ILE* 4.6 12.6 - - + +
345B TYR* 2.8 34.8 + - - -
349B GLN* 2.9 23.8 + - - -
354B ALA* 3.4 17.4 - - - +
355B ASN 2.8 12.5 + - - +
356B ILE* 3.9 20.1 - - + +
357B ASN* 2.9 24.3 + - - +
380B PHE* 3.5 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ALA 3.0 6.3 + - - +
210B SER* 3.1 26.1 + - - +
211B HIS 3.0 24.6 + - - +
326B ARG* 1.3 73.0 - - - +
328B ILE* 1.3 65.3 + - - +
329B TRP* 3.4 28.5 - + + -
357B ASN* 3.4 34.1 - - + -
359B SER* 3.8 25.8 - - - -
361B TYR* 4.9 1.3 - - - -
373B GLY 4.0 2.7 - - - -
376B PRO* 4.0 8.1 - - + -
377B SER* 3.8 21.3 - - - -
380B PHE* 3.5 31.6 - + + -
400B ALA* 3.8 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B HIS* 3.2 37.2 - - + +
214B THR* 4.5 11.0 - - - +
326B ARG* 4.3 9.8 - - + +
327B PHE* 1.3 82.6 - - - +
329B TRP* 1.3 62.1 + - - +
330B HIS* 5.7 1.6 - - + -
342B ALA* 5.6 7.0 - - + -
345B TYR* 4.3 12.3 - - + -
346B VAL* 4.1 21.1 - - + -
356B ILE* 4.0 39.0 - - + +
357B ASN 3.0 6.9 + - - +
358B PHE* 3.4 13.4 - - + -
359B SER* 2.7 32.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLU* 3.5 22.0 - - - -
182B GLY 4.3 5.4 - - - -
183B TYR* 3.5 28.6 - + + -
210B SER* 3.4 22.7 - - - -
211B HIS 3.2 34.3 + - - +
212B GLY* 3.0 33.0 - - - -
213B GLY 3.1 3.5 + - - -
327B PHE* 3.4 22.9 - + + -
328B ILE* 1.3 79.4 - - - +
330B HIS* 1.4 63.8 + - - +
358B PHE* 5.2 0.9 - - - -
359B SER* 3.4 22.0 - - - +
361B TYR* 3.7 18.8 - + + -
369B ALA* 2.9 32.3 + - + -
370B GLU 4.5 7.0 - - - -
373B GLY* 3.6 18.4 - - - -
374B LEU* 4.6 1.8 - - - -
377B SER* 3.5 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TYR* 5.8 0.4 - - - -
213B GLY* 3.5 13.8 - - - +
214B THR* 3.4 34.6 + - - -
328B ILE* 5.7 1.3 - - + -
329B TRP* 1.4 78.4 - - - +
331B ALA* 1.3 78.1 + - - +
332B ILE 3.3 0.7 + - - -
334B ASP* 3.6 11.2 + - + -
337B VAL* 3.2 34.3 - - + +
338B PRO 3.5 13.7 + - - -
339B TYR* 3.6 29.0 - + + -
342B ALA* 3.7 17.5 - - + +
358B PHE* 5.1 5.4 - - + -
359B SER 3.3 5.0 + - - +
360B PRO* 3.5 2.8 - - - +
361B TYR* 2.9 29.1 + - - -
369B ALA* 4.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TYR* 5.3 0.6 + - - -
330B HIS* 1.3 80.7 + - - +
332B ILE* 1.3 65.4 + - - +
334B ASP* 3.0 32.7 + - + +
339B TYR* 3.6 1.5 - - - +
361B TYR* 3.8 5.8 - - - -
364B ALA* 4.0 11.4 - - + -
365B GLU 3.4 35.0 - - - +
369B ALA* 3.6 16.0 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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