Contacts of the strand formed by residues 317 - 322 (chain A) in PDB entry 3UQU
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 ASP 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A CYS* 4.5 15.9 - - + +
270A TRP 3.5 8.0 - - - +
271A GLN* 4.5 8.5 + - - +
309A VAL 5.6 0.5 - - - +
315A SER* 3.1 30.4 + - - +
316A GLN* 1.3 83.9 + - - +
318A ASP* 1.3 65.8 + - - +
319A CYS* 3.8 11.0 + - - -
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Residues in contact with ASP 318 (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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269A CYS* 3.3 1.0 - - - -
270A TRP 2.8 34.9 + - - +
271A GLN 4.9 0.2 - - - +
272A ALA* 3.5 20.9 - - - +
273A GLY* 3.0 24.3 + - - -
275A THR* 4.4 7.6 + - - +
317A ASP* 1.3 73.2 - - - +
319A CYS* 1.3 60.9 + - - +
320A TYR* 3.5 34.8 + - + +
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Residues in contact with CYS 319 (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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267A LEU* 4.7 11.0 - - + -
268A VAL 3.5 0.7 - - - -
269A CYS* 2.1 47.8 - - - -
308A PRO* 3.4 7.3 - - - +
309A VAL* 2.9 47.5 + - + +
317A ASP* 3.8 13.9 + - - -
318A ASP* 1.3 72.0 - - - +
320A TYR* 1.3 62.4 + - - +
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Residues in contact with TYR 320 (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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261A PHE* 4.0 7.8 - - + -
267A LEU* 3.4 10.7 - - - -
268A VAL 2.8 29.9 + - - +
270A TRP* 3.7 20.9 - + + -
275A THR* 3.3 26.2 + - + -
277A TRP* 3.4 33.8 - + - -
306A LEU* 3.8 26.7 - - + -
307A ARG 3.4 18.8 - - - -
308A PRO* 3.7 22.3 - - + +
309A VAL* 4.4 1.3 - - - -
318A ASP* 3.5 35.5 + - + +
319A CYS* 1.3 74.0 - - - +
321A LYS* 1.4 59.2 + - - +
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Residues in contact with LYS 321 (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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233A ASN* 4.6 17.8 + - - +
261A PHE* 4.7 1.6 - - - -
264A GLY* 3.6 31.9 - - - +
266A GLN 5.1 0.7 - - - -
267A LEU* 3.6 22.4 - - + -
306A LEU* 3.4 3.8 - - - -
307A ARG* 2.8 37.9 + - + +
309A VAL* 4.0 13.4 - - + +
320A TYR* 1.4 73.7 - - - +
322A PHE* 1.3 75.3 + - - +
323A ALA* 3.5 5.2 + - + -
394A ZPX 4.6 12.5 - - - +
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Residues in contact with PHE 322 (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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233A ASN* 5.1 1.2 + - - -
245A VAL* 4.1 15.0 - - + -
248A ILE* 4.0 15.0 - - + -
261A PHE* 3.3 34.0 + - + +
262A TRP* 3.3 59.2 - + - -
264A GLY* 4.1 9.4 - - - -
266A GLN 5.3 0.2 + - - -
305A TYR* 3.8 24.9 - + - -
306A LEU* 3.8 20.2 - - + -
321A LYS* 1.3 85.6 - - - +
323A ALA* 1.4 58.3 + - - +
324A ILE* 3.3 51.1 + - + +
325A SER* 5.8 0.3 - - - -
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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