Contacts of the strand formed by residues 325 - 332 (chain A) in PDB entry 1OOA
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 ALA 325 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A GLU* 4.3 5.6 - - - +
316A TYR* 3.7 33.0 - - + +
321A ILE* 4.0 15.5 - - + +
323A LYS 3.6 1.1 + - - +
324A PRO* 1.3 73.6 - - - +
326A SER* 1.3 62.3 + - - +
327A VAL* 3.6 2.3 + - - +
346A LEU* 3.9 2.7 - - - -
347A TYR* 2.8 36.8 + - + +
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Residues in contact with SER 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU* 3.9 12.6 + - - +
324A PRO 4.2 0.6 + - - -
325A ALA* 1.3 72.7 - - - +
327A VAL* 1.3 70.0 + - - +
328A PHE* 5.5 5.3 - - - -
344A PRO* 4.7 9.4 - - - +
345A PHE 3.6 7.5 + - - -
346A LEU* 4.2 12.0 - - - +
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Residues in contact with VAL 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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282A PHE* 4.6 3.6 - - + -
283A TYR 3.5 11.7 - - - +
284A GLU* 3.8 18.4 - - + +
292A TRP* 4.5 4.0 - - + -
316A TYR* 3.8 29.2 - - + -
325A ALA 4.1 3.1 - - - +
326A SER* 1.3 84.4 + - - +
328A PHE* 1.3 79.8 + - - +
344A PRO* 3.5 4.7 - - - +
345A PHE* 2.8 46.4 + - + +
347A TYR* 3.7 26.7 - - + -
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Residues in contact with PHE 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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281A ARG 3.8 0.4 - - - +
282A PHE* 3.1 7.1 - - - +
283A TYR* 2.9 73.1 + + + +
284A GLU* 5.5 1.8 - - - -
285A GLU* 5.7 6.1 - - - -
326A SER* 5.5 4.7 - - - -
327A VAL* 1.3 88.9 - - - +
329A VAL* 1.3 64.2 + - - +
342A PRO* 4.0 18.4 - - + -
343A LYS 3.2 17.7 - - - -
344A PRO* 4.4 15.7 - - + -
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Residues in contact with VAL 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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250A ILE* 4.0 10.1 - - + +
253A MET* 4.5 20.6 - - + -
268A LEU* 5.2 0.2 - - + -
280A ILE* 3.6 27.6 - - + -
281A ARG 3.3 6.1 - - - +
282A PHE* 3.7 23.1 - - + -
328A PHE* 1.3 76.0 - - - +
330A GLN* 1.3 66.7 + - - +
342A PRO* 3.4 1.9 - - - +
343A LYS* 2.8 37.0 + - + +
344A PRO 4.7 2.0 - - - +
345A PHE* 3.2 37.5 - - + -
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Residues in contact with GLN 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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250A ILE* 3.9 10.3 - - - -
280A ILE* 3.6 3.8 - - - -
281A ARG* 2.6 86.5 + - + +
283A TYR* 3.7 19.4 + - + -
329A VAL* 1.3 79.6 - - - +
331A LEU* 1.3 64.4 + - - +
332A ARG* 5.1 0.2 - - + -
339A THR* 3.7 22.1 + - + +
340A SER* 3.4 26.6 + - - +
342A PRO* 4.2 10.3 - - + +
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Residues in contact with LEU 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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248A LEU* 4.2 6.7 - - + -
249A LYS 3.7 27.6 - - - +
250A ILE* 3.6 13.8 - - + +
268A LEU* 4.2 8.5 - - + -
270A CYS* 3.5 26.7 - - + -
273A VAL* 4.2 12.6 - - + -
278A ILE* 4.1 14.4 - - + -
279A GLN 3.6 1.8 - - - -
280A ILE* 3.6 28.7 - - + -
309A ILE* 4.1 15.5 - - + -
330A GLN* 1.3 74.8 - - - +
332A ARG* 1.3 60.9 + - - +
339A THR* 3.2 6.3 - - - -
340A SER* 3.1 35.8 + - - +
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Residues in contact with ARG 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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248A LEU* 4.6 0.4 - - - -
278A ILE* 3.5 6.2 - - - +
279A GLN* 2.7 75.7 + - + +
281A ARG* 3.7 31.3 - - + +
293A GLU* 3.6 19.8 + - - -
295A PHE* 3.5 21.6 - - - -
330A GLN* 5.1 0.4 - - + -
331A LEU* 1.3 77.5 - - - +
333A ARG* 1.3 67.7 + - - +
337A LEU* 3.3 35.2 + - + +
338A GLU 3.2 11.9 - - - +
339A THR* 4.0 14.3 - - + +
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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