Contacts of the strand formed by residues 356 - 362 (chain A) in PDB entry 3INH
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 GLN 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A TRP* 4.6 9.5 - - + -
266A VAL* 5.5 0.7 - - - +
350A MET* 3.8 3.5 - - - +
351A GLY* 2.9 23.4 + - - -
353A VAL* 2.8 46.9 + - + +
354A THR 4.0 3.8 - - - +
355A ASN* 1.3 89.6 + - - +
357A SER* 1.3 62.8 + - - +
435A PRO* 3.6 25.7 - - + +
436A PHE 3.5 4.7 - - - +
437A VAL* 4.2 16.5 - - + +
438A THR* 6.0 1.1 - - - -
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Residues in contact with SER 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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251A TRP* 5.6 1.3 - - - -
266A VAL* 3.6 25.7 - - - +
348A TYR* 3.8 12.5 - - - -
349A LEU 3.1 16.6 - - - -
350A MET* 4.5 0.2 - - - -
351A GLY* 3.8 3.8 - - - +
356A GLN* 1.3 78.3 - - - +
358A PHE* 1.3 60.6 + - - +
435A PRO* 3.4 7.4 - - - +
436A PHE* 2.7 49.6 + - - +
438A THR* 5.1 5.4 - - - +
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Residues in contact with PHE 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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251A TRP* 3.4 61.7 - + + -
252A TYR 3.5 24.7 - - - -
253A THR* 3.8 13.9 - - - -
347A LEU 3.7 0.3 - - - +
348A TYR* 3.3 4.2 - - - -
349A LEU* 2.7 64.8 + - + +
350A MET 4.0 2.0 - - - -
351A GLY* 4.6 2.9 - - - -
357A SER* 1.3 77.0 - - - +
359A ARG* 1.3 64.6 + - - +
360A ILE* 4.2 3.4 - - + -
416A PHE* 4.1 18.4 - + + -
432A VAL* 4.0 10.1 - - + -
433A GLU 3.3 13.9 - - - +
434A GLY* 4.0 1.3 - - - -
436A PHE* 4.4 1.3 - - - -
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Residues in contact with ARG 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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269A GLU* 4.0 6.1 + - - -
346A SER* 4.3 9.0 - - - -
347A LEU 3.2 8.7 - - - +
348A TYR* 2.9 49.2 + - + +
358A PHE* 1.3 74.6 - - - +
360A ILE* 1.3 62.1 + - - +
361A THR* 4.0 15.0 + - - +
431A ALA 3.7 0.6 - - - +
432A VAL* 3.3 5.2 - - - +
433A GLU* 2.8 71.3 + - + +
436A PHE* 3.3 29.5 - - + -
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Residues in contact with ILE 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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345A ILE 3.7 1.6 - - - +
346A SER* 3.4 1.6 - - - -
347A LEU* 2.9 51.2 + - + +
349A LEU* 4.2 7.4 - - + -
358A PHE* 4.2 10.8 - - + -
359A ARG* 1.3 77.2 - - - +
361A THR* 1.3 61.3 + - - +
362A ILE* 4.1 3.2 + - + +
395A MET* 3.7 30.5 - - + -
399A ILE* 4.0 17.3 - - + -
403A PHE* 3.6 16.6 - - + -
416A PHE* 4.0 36.6 - - + -
431A ALA 3.3 3.8 - - - -
432A VAL* 4.1 11.2 - - + -
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Residues in contact with THR 361 (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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344A VAL* 3.8 31.9 - - + -
345A ILE 3.4 3.4 - - - +
346A SER* 2.8 24.8 + - - +
359A ARG* 4.0 15.6 + - - +
360A ILE* 1.3 73.3 - - - +
362A ILE* 1.3 64.0 + - - +
363A LEU* 5.2 0.9 - - + -
403A PHE* 3.6 2.4 - - - -
429A THR 5.2 5.6 - - - +
430A ALA* 3.3 11.8 - - - +
431A ALA* 2.9 43.3 + - - +
433A GLU* 4.7 0.9 + - - -
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Residues in contact with ILE 362 (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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296A LEU* 4.8 2.9 - - + -
344A VAL* 3.4 6.9 - - - +
345A ILE* 2.8 57.7 + - + +
347A LEU* 6.4 0.4 - - + -
360A ILE* 4.8 4.7 - - + +
361A THR* 1.3 78.5 - - - +
363A LEU* 1.3 64.2 + - - +
366A GLN* 3.3 32.1 - - + +
367A TYR* 3.9 31.1 - - + -
398A VAL 5.1 0.9 - - - +
399A ILE* 3.5 35.9 - - + +
403A PHE* 3.7 17.7 - - + -
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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