Contacts of the strand formed by residues 326 - 333 (chain A) in PDB entry 4UU5
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 GLY 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A GLU* 3.7 10.3 - - - -
261A LYS 2.8 35.8 + - - -
325A HIS* 1.3 84.9 - - - +
327A THR* 1.3 64.7 + - - -
328A LEU* 3.3 4.0 + - - +
1343A PUN 6.5 0.7 - - - -
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Residues in contact with THR 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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258A ARG* 4.1 37.0 - - + +
259A ILE 3.8 2.7 - - - +
260A GLU* 2.6 29.3 + - - +
305A ASN* 3.4 17.5 + - - +
325A HIS 4.2 0.5 + - - +
326A GLY* 1.3 71.1 - - - -
328A LEU* 1.3 62.5 + - - +
329A THR* 4.0 3.8 + - - +
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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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257A VAL 3.4 2.1 - - - +
258A ARG* 3.3 4.0 - - - -
259A ILE* 2.8 40.8 + - + +
261A LYS* 4.0 21.5 - - + -
267A LEU* 5.1 4.7 - - + -
304A ILE* 4.2 9.4 - - + -
305A ASN* 3.4 16.2 - - - +
321A LEU* 3.7 29.6 - - + -
324A MET* 4.2 15.0 - - + -
325A HIS 4.0 16.8 - - - +
326A GLY 3.8 10.8 - - - +
327A THR* 1.3 80.4 - - - +
329A THR* 1.3 62.1 + - - +
330A PHE* 3.8 24.2 + - + -
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Residues in contact with THR 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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256A ILE* 3.5 29.6 - - + -
257A VAL 3.3 4.9 - - - +
258A ARG* 3.6 21.3 - - + +
303A GLU* 3.9 1.7 - - - +
304A ILE* 3.4 3.4 - - - -
305A ASN* 2.7 39.2 + - - -
327A THR* 4.5 5.4 + - - +
328A LEU* 1.3 70.5 - - - +
330A PHE* 1.3 61.9 + - - +
331A VAL* 4.0 5.7 + - + +
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Residues in contact with PHE 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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255A LYS 3.6 1.2 - - - +
256A ILE* 3.3 8.2 - - - +
257A VAL* 2.8 50.4 + - + +
259A ILE* 4.5 10.1 - - + -
267A LEU* 3.8 30.1 - - + -
280A ILE* 5.1 0.4 - - + -
295A LEU* 4.2 13.9 - - + -
301A VAL* 4.0 18.4 - - + -
303A GLU 3.5 4.9 - - - +
304A ILE* 3.6 33.7 - - + +
321A LEU* 4.9 1.3 - - + -
328A LEU* 3.9 34.1 - - + -
329A THR* 1.3 74.4 - - - +
331A VAL* 1.3 61.3 + - - +
332A LEU* 4.0 16.4 - - + -
1406B ILE* 4.6 13.5 - - + -
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Residues in contact with VAL 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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254A VAL* 4.1 29.8 - - + -
255A LYS 3.6 3.1 - - - +
256A ILE* 4.6 20.0 - - + +
301A VAL* 3.8 2.3 - - - -
302A LEU* 2.8 43.2 + - + +
303A GLU* 2.9 47.1 + - + +
329A THR* 5.0 4.9 - - + +
330A PHE* 1.3 74.9 - - - +
332A LEU* 1.3 57.3 + - - +
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Residues in contact with LEU 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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254A VAL* 3.3 9.3 - - - +
255A LYS* 2.8 47.0 + - + +
257A VAL* 4.0 19.5 - - + -
294A LEU 4.0 5.8 - - - +
295A LEU* 3.8 24.0 - - + -
299A ASP* 3.9 22.7 - - + +
300A GLU 3.1 15.9 - - - +
301A VAL* 3.9 22.9 - - + -
302A LEU* 4.6 1.6 - - - +
330A PHE* 4.0 21.3 - - + -
331A VAL* 1.3 76.8 - - - +
333A ILE* 1.3 69.6 + - - +
334A PRO* 3.6 0.8 - - - +
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Residues in contact with ILE 333 (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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250A SER* 4.1 37.2 - - - +
253A THR* 4.2 16.4 - - + +
254A VAL* 4.4 2.5 - - + -
298A GLY 4.3 0.7 - - - +
299A ASP* 3.5 0.2 - - - -
300A GLU* 2.9 54.3 + - + +
302A LEU* 3.9 29.1 - - + +
332A LEU* 1.3 76.8 - - - +
334A PRO* 1.3 78.4 - - + +
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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