Contacts of the strand formed by residues 326 - 331 (chain A) in PDB entry 5INQ
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 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A THR* 5.0 9.0 + - + +
129A TRP* 5.2 0.9 - - - -
130A ASN 4.3 6.4 + - - -
161A GLN* 4.1 6.4 - - - +
271A GLY 3.4 7.6 - - - +
272A ASP* 3.4 24.5 + - - +
306A THR* 2.7 33.7 + - - +
324A ARG* 4.1 12.6 + - - +
325A PHE* 1.3 77.7 - - - +
327A ARG* 1.3 65.3 + - - +
359A HIS* 2.9 30.0 + - - +
360A TRP 4.6 6.5 - - - +
362A LEU* 3.5 25.4 - - + +
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Residues in contact with ARG 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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128A THR* 5.0 0.7 - - - +
269A PHE* 4.0 5.9 - - - -
270A ALA* 3.5 2.6 - - - -
271A GLY 3.1 30.2 + - - +
273A THR* 3.8 22.9 + - + +
275A LEU* 3.4 24.9 + - - -
277A ASP* 3.1 25.9 + - - +
280A VAL* 3.7 25.3 - - - +
292A ASP* 3.9 8.2 + - - +
295A GLU* 5.7 0.2 + - - -
324A ARG* 2.9 66.1 + - - +
325A PHE 3.7 0.4 + - - -
326A ASP* 1.3 81.6 - - - +
328A ILE* 1.3 65.2 + - - +
329A PHE* 4.0 23.5 - - + -
362A LEU* 4.5 1.8 - - - +
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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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126A PHE* 3.7 40.6 - - + -
128A THR* 4.3 4.9 - - + -
268A ILE* 4.3 7.6 - - + -
269A PHE 3.3 9.4 - - - +
270A ALA* 3.9 7.0 - - + -
292A ASP* 3.3 9.5 + - - +
293A ALA* 3.0 44.2 + - + -
327A ARG* 1.3 78.9 - - - +
329A PHE* 1.3 66.6 + - - +
330A PHE* 5.0 4.0 - - + -
342A LEU* 3.6 31.9 - - + -
362A LEU* 4.2 16.6 - - + +
364A CYS* 3.8 8.7 - - + -
366A LEU* 5.6 2.5 - - + -
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Residues in contact with PHE 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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251A LEU* 3.9 23.1 - - + -
254A VAL* 5.0 2.2 - - + -
255A LEU* 4.4 11.9 - - + -
258A MET* 3.6 16.6 - - + +
268A ILE* 3.6 2.8 - - - +
269A PHE* 2.8 62.4 + + + +
273A THR* 4.5 3.1 - - + -
275A LEU* 4.3 12.1 - - + -
280A VAL* 5.7 2.2 - - + -
286A LEU* 4.1 24.2 - - + -
290A VAL* 4.0 6.3 - - + -
291A PHE 3.1 5.6 - - - +
292A ASP* 3.7 29.4 - - + -
327A ARG* 4.0 26.9 - - + -
328A ILE* 1.3 79.6 - - - +
330A PHE* 1.3 65.0 + - - +
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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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258A MET* 3.8 3.8 - - - -
267A VAL 3.4 7.9 - - - +
268A ILE* 4.4 6.7 - - + -
289A ASN 3.9 0.9 - - - +
290A VAL* 3.4 3.1 - - - -
291A PHE* 2.8 71.7 + + + -
293A ALA* 4.0 21.1 - - + -
296A PHE* 4.1 12.3 - + + -
328A ILE* 5.0 3.4 - - + -
329A PHE* 1.3 78.7 - - - +
331A ARG* 1.3 61.3 + - - +
332A ALA* 4.6 5.6 - - + -
337A LEU* 3.5 49.6 - - + -
339A PRO* 3.4 36.6 - - + -
366A LEU* 5.2 3.8 - - + -
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Residues in contact with ARG 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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258A MET* 3.1 37.0 + - + +
259A GLN* 3.3 13.4 + - - +
261A ALA 2.9 21.0 + - - -
262A PRO 2.7 28.1 + - - -
263A ASP* 3.9 13.4 + - - +
265A THR 3.0 19.3 + - - +
266A THR* 4.1 2.6 - - - +
267A VAL* 3.0 42.5 + - + +
289A ASN* 3.4 41.9 - - + +
290A VAL* 4.1 11.9 - - + -
330A PHE* 1.3 74.2 - - - +
332A ALA* 1.3 66.6 + - - +
333A GLU 5.8 0.2 - - - +
337A LEU* 5.2 0.2 - - - -
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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