Contacts of the strand formed by residues 355 - 360 (chain A) in PDB entry 3P3W
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 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A PRO* 5.1 2.9 - - + -
116A ALA 4.1 10.1 - - - +
117A LEU* 4.5 10.3 - - + -
120A ALA* 3.9 22.4 - - + -
222A LEU* 5.0 2.5 - - + -
242A PHE* 4.4 19.3 - - + -
243A GLN 3.5 19.5 - - - +
244A ILE* 4.6 11.7 - - + -
353A TYR* 3.5 36.1 - - + -
354A THR* 1.3 72.3 - - - +
356A ASP* 1.3 71.7 + - - +
357A VAL* 3.4 4.3 + - + +
370A TYR* 3.4 1.0 - - - -
371A TRP* 2.8 53.8 + - + +
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Residues in contact with ASP 356 (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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242A PHE* 4.0 1.9 - - - -
243A GLN 2.8 35.6 + - - +
244A ILE 3.9 6.8 - - - +
245A VAL 3.6 10.7 - - - +
246A ASN* 3.4 36.3 + - - +
354A THR* 4.2 15.2 - - - +
355A ILE* 1.3 72.2 - - - +
357A VAL* 1.3 62.3 + - - +
358A TYR* 3.5 25.3 + - + +
369A GLY 3.8 4.9 - - - +
370A TYR* 4.7 4.7 - - - +
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Residues in contact with VAL 357 (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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120A ALA* 6.2 0.4 - - + -
124A LEU* 3.8 30.1 - - + -
128A TYR* 5.2 0.2 - - - +
240A THR* 4.1 13.2 - - + -
241A GLY 3.9 9.9 - - - +
242A PHE* 5.0 6.3 - - + +
355A ILE* 3.8 12.6 - - + +
356A ASP* 1.3 71.7 - - - +
358A TYR* 1.3 58.2 + - - +
367A LYS* 3.6 5.5 - - - +
368A ALA* 2.8 35.8 + - + -
369A GLY 2.7 24.0 + - - +
371A TRP* 4.4 9.9 - - + -
377A PHE* 3.9 32.1 - - + -
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Residues in contact with TYR 358 (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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224A PHE* 4.1 21.2 - + + -
239A ILE 3.7 1.0 - - - +
240A THR* 3.5 5.5 - - - +
241A GLY 2.9 37.1 + - - +
243A GLN* 3.5 48.5 + - + -
245A VAL 3.9 14.2 + - - -
246A ASN* 4.2 10.9 + - - -
247A ASN* 5.0 3.5 + - - +
356A ASP* 3.5 27.4 - - + +
357A VAL* 1.3 74.5 - - - +
359A GLU* 1.3 62.3 + - - +
360A MET* 4.0 2.9 - - + -
366A ARG 3.9 3.4 - - - +
367A LYS* 3.9 30.3 - - + -
368A ALA* 4.5 0.2 - - - -
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Residues in contact with GLU 359 (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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127A TYR* 4.6 8.3 + - - -
128A TYR* 2.7 39.8 + - - +
216A HIS* 6.1 1.1 - - + -
239A ILE 3.6 3.1 - - - +
240A THR* 4.2 6.7 - - + +
358A TYR* 1.3 73.8 - - - +
360A MET* 1.3 62.2 + - - +
361A LYS* 3.4 32.7 + - + +
364A GLY 4.1 1.0 - - - +
365A SER* 3.8 1.7 - - - -
366A ARG* 3.0 54.8 + - - +
368A ALA* 3.6 27.3 - - + +
377A PHE* 5.1 1.9 - - - -
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Residues in contact with MET 360 (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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224A PHE* 3.6 21.1 - - + -
229A LEU* 3.5 33.4 - - + -
233A MET* 3.7 37.6 - - + +
237A ALA 3.5 3.8 - - - +
239A ILE* 2.7 51.4 + - + +
358A TYR* 4.0 3.1 - - + -
359A GLU* 1.3 73.9 - - - +
361A LYS* 1.3 59.4 + - - +
364A GLY 4.0 2.2 - - - -
365A SER* 3.5 25.1 - - - +
366A ARG 5.3 0.7 - - - +
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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