Contacts of the strand formed by residues 336 - 341 (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 ILE 336 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A ILE* 3.8 37.0 - - + -
328A VAL 3.6 2.2 - - - +
329A GLY 4.0 3.8 - - - -
330A GLY* 3.6 31.2 - - - +
335A GLY* 1.3 73.8 - - - -
337A PHE* 1.3 61.7 + - - +
358A GLN* 3.3 9.1 - - - +
359A ILE* 2.9 46.7 + - + +
367A LEU* 3.9 20.3 + - + +
370A ALA* 4.0 5.2 - - + +
371A SER 3.9 6.1 - - - +
372A HIS* 4.2 4.5 - - - -
375A ALA* 3.5 29.4 - - + -
379A LEU* 5.2 2.0 - - + -
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Residues in contact with PHE 337 (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* 3.1 9.1 - - - -
328A VAL* 2.9 39.2 + - + +
334A GLU 3.6 19.3 - - - -
335A GLY 3.5 21.3 - - - -
336A ILE* 1.3 75.4 - - - +
338A ILE* 1.3 63.0 + - - +
356A GLY 4.1 8.5 - - - -
357A ASP 3.3 4.7 - - - +
358A GLN* 3.8 39.7 - - + -
359A ILE* 5.3 0.2 - - - -
393A LYS* 4.0 9.6 - - + -
396A GLU* 3.8 31.6 - - + -
397A TYR* 3.9 26.7 - + + -
400A PHE* 3.7 27.6 - + - -
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Residues in contact with ILE 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A PHE* 4.0 19.7 - - + -
326A ASN 3.5 11.0 - - - +
327A ILE* 4.6 0.2 - - - +
337A PHE* 1.3 72.4 - - - +
339A SER* 1.3 60.7 + - - +
340A PHE 4.1 4.5 - - - +
341A ILE* 3.7 28.7 - - + -
353A LEU* 4.0 36.8 - - + -
354A ARG 3.8 14.8 - - - +
355A LYS* 3.5 1.5 - - - -
356A GLY 3.0 26.0 + - - -
357A ASP* 2.9 22.2 + - + +
359A ILE* 3.7 29.4 - - + -
397A TYR* 3.6 5.8 - - - -
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Residues in contact with SER 339 (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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326A ASN* 3.0 10.0 + - - +
328A VAL* 3.7 18.6 - - - -
337A PHE 3.5 1.0 + - - -
338A ILE* 1.3 73.5 - - - +
340A PHE* 1.3 65.6 + - - +
355A LYS* 3.4 25.8 - - - +
397A TYR* 3.7 20.7 + - - -
401A GLU* 5.9 0.2 - - - -
422B GLU* 2.4 36.9 + - - -
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Residues in contact with PHE 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A PHE* 3.2 7.1 - - - +
326A ASN* 2.9 52.9 + - - +
338A ILE* 3.8 1.2 - - - +
339A SER* 1.3 83.6 + - - +
341A ILE* 1.3 73.7 + - - +
342A LEU* 3.7 26.2 - - + -
343A ALA 5.4 0.7 - - - -
355A LYS* 5.5 1.8 - - - -
422B GLU* 5.9 0.2 - - - -
424B TRP* 3.6 25.6 - + - -
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Residues in contact with ILE 341 (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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324A GLY 3.8 7.4 - - - +
325A PHE* 4.1 4.9 - - + -
338A ILE* 3.7 14.4 - - + -
340A PHE* 1.3 90.9 - - - +
342A LEU* 1.3 66.0 + - - +
343A ALA 3.5 2.4 + - - -
347A ALA* 4.2 4.3 - - + -
348A ASP* 3.7 36.3 - - + +
353A LEU* 3.5 35.4 - - + +
354A ARG* 3.6 22.0 - - - +
355A LYS* 3.9 3.8 - - + +
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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