Contacts of the strand formed by residues 344 - 349 (chain A) in PDB entry 4H3I
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 344 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A VAL* 4.9 3.1 - - + -
268A GLU 3.5 8.7 - - - +
269A ILE* 3.9 19.3 - - + -
295A LEU* 5.1 7.6 - - + -
305A ALA* 6.4 0.4 - - + -
309A ILE* 3.8 15.3 - - + -
342A PRO 4.4 1.6 - - - +
343A VAL* 1.3 79.5 - - - +
345A SER* 1.3 69.8 + - - +
346A LEU* 4.3 16.1 + - + +
359A ILE 3.7 0.7 - - - +
360A THR* 3.2 1.8 - - - -
361A ILE* 2.9 48.1 + - + +
366A TYR* 3.6 24.0 - - + -
385A ILE* 3.5 31.4 - - + -
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Residues in contact with SER 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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266A ARG 4.0 0.2 - - - +
267A VAL* 3.4 6.2 - - - +
268A GLU* 3.0 46.9 + - - +
271A GLY 5.7 1.2 + - - -
343A VAL* 4.8 4.3 - - - +
344A ILE* 1.3 73.4 - - - +
346A LEU* 1.3 65.6 + - - +
347A TYR* 4.1 19.4 - - - -
358A ARG* 4.5 9.2 + - - -
359A ILE 3.2 5.4 - - - -
360A THR* 2.7 29.6 + - - +
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Residues in contact with LEU 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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264A ILE* 4.3 25.8 - - + -
266A ARG 3.7 2.2 - - - -
267A VAL* 3.9 26.9 - - + -
295A LEU* 4.7 11.0 - - + -
297A LEU* 5.5 9.2 - - + -
344A ILE* 4.6 12.3 - - + +
345A SER* 1.3 78.9 - - - +
347A TYR* 1.3 62.7 + - - +
348A LEU* 3.8 7.5 + - + +
358A ARG* 3.4 1.0 - - - -
359A ILE* 2.9 41.4 + - + +
392A THR* 5.6 0.2 - - + -
394A MET* 4.4 20.0 - - + -
398A ILE* 3.9 27.6 - - + -
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Residues in contact with TYR 347 (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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264A ILE* 3.3 8.7 - - - +
265A VAL* 2.8 34.2 + - + -
266A ARG* 2.8 53.3 + - + +
268A GLU* 2.5 40.6 + - + -
345A SER* 4.2 7.4 - - - -
346A LEU* 1.3 73.0 - - - +
348A LEU* 1.3 60.2 + - - +
356A SER* 4.0 10.8 - - - +
357A PHE 3.2 5.4 - - - +
358A ARG* 2.9 46.6 + - + -
435A PHE* 3.7 37.6 - + + -
437A THR* 5.5 0.9 - - - -
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Residues in contact with LEU 348 (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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252A THR* 3.6 15.3 - - + +
262A VAL* 4.7 11.7 - - + -
263A ILE 3.6 8.1 - - - +
264A ILE* 3.6 30.5 - - + -
265A VAL* 4.3 1.6 - - - -
346A LEU* 4.1 11.9 - - + +
347A TYR* 1.3 78.0 - - - +
349A MET* 1.3 65.6 + - - +
356A SER* 3.2 6.6 - - - -
357A PHE* 2.8 58.1 + - + -
359A ILE* 4.3 13.0 - - + -
394A MET* 4.7 7.0 - - + -
415A PHE* 3.7 29.2 - - + -
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Residues in contact with MET 349 (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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252A THR* 2.6 37.9 + - - +
253A PRO* 4.1 17.3 - - + -
263A ILE* 3.1 45.4 + - + +
265A VAL* 4.2 4.0 - - + +
348A LEU* 1.3 71.8 - - - +
350A GLY* 1.3 71.7 + - - +
357A PHE* 3.8 0.7 - - - -
440A MET* 3.5 61.2 - - + +
441A GLU* 3.7 23.6 - - - +
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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