Contacts of the strand formed by residues 325 - 329 (chain A) in PDB entry 1TP5
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 PHE 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A ILE* 5.1 0.2 - - + -
323A LEU* 3.8 23.6 - - + -
324A GLY* 1.3 78.1 - - - +
326A ASN* 1.3 76.5 + - - +
327A ILE* 3.6 18.2 - - + -
338A ILE* 4.0 18.2 - - + -
340A PHE 3.2 15.0 - - - +
341A ILE* 4.1 13.7 - - + +
347A ALA* 3.7 19.1 - - + -
353A LEU* 4.4 11.2 - - + -
359A ILE* 4.5 7.9 - - + -
379A LEU* 4.2 20.4 - - + -
388A ILE* 4.4 16.8 - - + -
424B TRP* 3.2 4.1 - - - -
425B VAL* 2.9 47.2 + - + +
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Residues in contact with ASN 326 (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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325A PHE* 1.3 76.6 - - - +
327A ILE* 1.3 62.9 + - - +
338A ILE* 3.5 6.6 - - - -
339A SER* 3.0 25.7 + - - +
340A PHE* 2.9 32.0 + - + +
422B GLU* 3.2 28.3 - - + +
423B THR 3.2 9.4 - - - +
424B TRP* 2.5 57.9 - - - +
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Residues in contact with ILE 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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325A PHE* 3.6 28.7 - - + -
326A ASN* 1.3 73.8 - - - +
328A VAL* 1.3 58.6 + - - +
336A ILE* 3.8 31.9 - - + -
337A PHE 3.1 12.1 - - - +
338A ILE* 4.7 0.2 - - - -
359A ILE* 4.9 2.5 - - + -
372A HIS* 3.2 36.8 - - + +
375A ALA* 4.0 6.5 - - + -
376A ALA* 4.0 31.2 - - + +
379A LEU* 4.2 9.9 - - + -
422B GLU* 2.7 22.2 - - - +
423B THR* 3.1 16.6 + - - +
425B VAL* 4.8 3.6 - - + -
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Residues in contact with VAL 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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327A ILE* 1.3 69.6 - - - +
329A GLY* 1.3 60.1 + - - +
335A GLY 3.9 0.2 - - - +
336A ILE* 3.6 4.3 - - - +
337A PHE* 2.9 46.2 + - + +
339A SER* 3.7 7.6 - - - -
372A HIS* 4.2 2.5 - - - -
397A TYR* 4.0 23.8 - - + -
400A PHE* 4.2 25.4 - - + -
421B LYS 4.1 12.6 - - - +
422B GLU* 3.0 34.3 - - - +
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Residues in contact with GLY 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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328A VAL* 1.3 75.6 - - - +
330A GLY* 1.3 59.6 + - - -
331A GLU* 3.4 3.5 + - - +
334A GLU* 3.3 19.1 - - - -
335A GLY 3.3 8.7 - - - -
336A ILE* 4.0 3.4 - - - -
372A HIS* 3.0 26.1 + - - +
400A PHE* 4.0 13.6 - - - -
421B LYS* 4.7 2.4 + - - +
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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