Contacts of the strand formed by residues 341 - 346 (chain A) in PDB entry 3TPJ
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 341 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A LEU 3.9 6.4 - - - +
153A GLN* 4.3 5.9 - - - -
154A LEU 4.5 0.7 + - - +
298A ILE* 3.6 29.2 - - + -
299A THR 3.5 22.2 - - - -
300A ILE* 3.5 17.9 - - + -
337A ILE* 3.0 34.8 - - + -
338A MET* 2.9 16.0 + - - +
339A GLU 3.3 0.8 - - - -
340A GLY* 1.3 88.9 - - - +
342A TYR* 1.3 66.0 + - - +
343A VAL* 3.8 14.2 + - + +
354A PHE* 4.1 13.7 - + + -
355A ALA 3.2 10.1 - - - +
356A VAL* 4.3 1.1 - - - -
357A SER* 3.6 10.3 - - - -
368A ALA* 4.2 4.7 - - + -
369A ALA 3.4 22.0 - - - -
370A VAL* 3.5 22.4 - - + -
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Residues in contact with TYR 342 (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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151A SER* 2.5 37.4 + - - -
152A LEU 3.6 19.1 - - - -
153A GLN* 3.8 12.3 - - + +
175A ILE* 3.8 5.2 - - + +
179A ILE* 3.4 16.8 - - + -
180A ASP 2.9 25.1 + - - -
183A LEU* 3.6 31.9 - - + +
184A TYR* 3.3 50.5 - + + -
188A LEU* 4.3 4.5 - - + +
341A PHE* 1.3 71.6 - - - +
343A VAL* 1.3 59.2 + - - +
344A VAL* 4.1 12.3 + - + -
353A GLY 3.6 1.0 - - - +
354A PHE* 3.5 4.3 - - - -
355A ALA* 2.8 28.7 + - + +
357A SER* 3.8 4.5 - - - -
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Residues in contact with VAL 343 (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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151A SER* 3.3 3.3 - - - -
152A LEU 2.8 39.7 + - - +
227A VAL* 4.6 2.9 - - + -
338A MET* 4.1 26.0 - - + -
341A PHE* 4.0 22.2 - - + +
342A TYR* 1.3 76.6 - - - +
344A VAL* 1.3 63.8 + - - +
345A PHE* 3.5 30.1 - - + -
352A ILE* 3.7 22.7 - - + -
353A GLY 3.2 3.6 - - - +
354A PHE* 4.0 18.8 - - + -
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Residues in contact with VAL 344 (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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149A LEU* 4.1 31.4 - - + -
150A PHE 3.9 2.2 - - - +
151A SER* 4.0 11.9 - - - -
179A ILE* 4.1 20.2 - - + -
188A LEU* 3.7 28.3 - - + -
190A TYR* 4.3 6.1 - - + +
342A TYR* 4.2 13.2 - - + -
343A VAL* 1.3 73.7 - - - +
345A PHE* 1.3 61.6 + - - +
346A ASP* 3.3 11.1 + - + +
351A ARG 3.8 0.2 - - - +
352A ILE* 3.1 10.0 - - - +
353A GLY* 2.8 42.4 + - - +
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Residues in contact with PHE 345 (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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33A THR* 3.8 23.1 - - + -
149A LEU* 3.5 1.4 - - - -
150A PHE* 2.7 68.6 + + + +
152A LEU* 3.8 19.7 - - + -
193A ILE* 5.6 0.7 - - - -
199A TYR* 3.8 41.7 - + + -
227A VAL* 3.9 22.4 - - + -
338A MET* 3.9 6.5 - - + -
343A VAL* 3.5 35.0 - - + -
344A VAL* 1.3 70.7 - - - +
346A ASP* 1.3 60.9 + - - +
347A ARG* 3.1 11.9 + - - +
351A ARG 4.0 2.2 - - - -
352A ILE* 4.3 9.9 - - + -
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Residues in contact with ASP 346 (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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148A ASN 4.5 0.2 - - - +
149A LEU* 3.8 27.6 - - + +
190A TYR* 4.4 3.7 + - + -
193A ILE* 4.8 0.9 - - - -
344A VAL* 3.3 9.1 + - + -
345A PHE* 1.3 70.2 - - - +
347A ARG* 1.3 57.9 + - - +
348A ALA* 3.5 9.4 + - - +
349A ARG* 3.1 28.7 + - - +
350A LYS 2.9 22.7 + - - -
351A ARG* 2.9 62.0 + - + +
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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