Contacts of the strand formed by residues 351 - 358 (chain A) in PDB entry 3IW4
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 GLY 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A LYS* 3.2 4.4 - - - +
348A GLY 2.7 40.6 + - - +
349A SER 2.9 4.8 + - - -
350A PHE* 1.3 81.7 - - - +
352A LYS* 1.3 59.7 + - - -
368A LYS* 4.7 0.2 - - - -
370A LEU* 4.2 19.7 - - - -
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Residues in contact with LYS 352 (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* 4.6 8.7 - - + +
346A GLY 3.4 9.0 - - - +
347A LYS* 3.8 38.7 - - + +
350A PHE 4.0 1.2 + - - -
351A GLY* 1.3 73.0 - - - +
353A VAL* 1.3 68.8 + - - +
354A MET* 3.2 37.2 - - + +
367A ILE 3.5 1.2 - - - +
368A LYS* 3.2 2.9 - - - +
369A ILE* 2.8 51.4 + - + +
412A ARG* 5.9 1.2 - - - +
636A VAL 5.7 1.0 + - - -
637A LEU* 5.0 9.9 - - - +
638A TPO 4.6 15.0 + - - -
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Residues in contact with VAL 353 (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* 3.6 4.2 - - - +
345A LEU* 2.6 39.2 + - + -
346A GLY 3.0 12.2 + - - +
350A PHE* 4.2 11.4 - - + -
352A LYS* 1.3 79.2 - - - +
354A MET* 1.3 58.0 + - - +
366A ALA* 3.6 30.3 - - + -
367A ILE 3.4 7.0 - - - +
368A LYS* 4.3 6.3 - - + +
901A LW4 3.6 59.9 - - + -
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Residues in contact with MET 354 (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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341A PHE* 4.0 33.9 - - + -
343A MET 3.0 23.6 - - - +
344A VAL* 3.6 22.4 - - - -
345A LEU* 3.8 4.0 - - - -
352A LYS* 3.2 34.8 - - + +
353A VAL* 1.3 73.9 - - - +
355A LEU* 1.3 68.2 + - - +
356A ALA* 3.7 0.4 + - + -
365A TYR 3.7 0.7 - - - +
366A ALA* 3.3 4.7 - - - -
367A ILE* 2.9 37.3 + - + +
369A ILE* 3.5 19.7 - - + -
635A PRO* 4.4 17.9 - - + -
637A LEU* 4.9 3.8 - - + -
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Residues in contact with LEU 355 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342A LEU* 3.1 36.6 + - + +
343A MET* 2.8 33.0 + - + +
345A LEU* 3.5 22.2 - - + +
354A MET* 1.3 74.7 - - - +
356A ALA* 1.3 62.1 + - - +
364A LEU* 4.4 17.0 - - + -
365A TYR 3.4 16.8 - - - +
419A TYR* 3.5 56.5 - - + +
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Residues in contact with ALA 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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339A PHE* 4.5 7.2 - - + -
340A ASN 3.4 17.0 - - - +
341A PHE* 3.9 20.2 - - + -
342A LEU* 4.0 4.9 - - - -
354A MET 4.7 0.2 - - - +
355A LEU* 1.3 78.7 - - - +
357A ASP* 1.3 60.6 + - - +
364A LEU* 3.3 9.8 - - - +
365A TYR* 2.9 33.1 + - - +
367A ILE* 4.0 21.5 - - + -
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Residues in contact with ASP 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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339A PHE* 3.3 9.1 - - - -
340A ASN* 3.0 47.5 + - - +
342A LEU* 4.4 13.9 - - - +
356A ALA* 1.3 74.5 - - - +
358A ARG* 1.3 70.8 + - - +
359A LYS* 3.2 2.5 + - - -
360A GLY 5.9 0.4 - - - -
361A THR 4.4 7.3 - - - +
362A GLU 5.1 0.2 - - - -
363A GLU 3.2 12.6 - - - +
364A LEU* 3.5 15.6 - - + +
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Residues in contact with ARG 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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332A ASP* 3.4 32.7 + - - -
333A ARG 3.9 4.9 + - - -
334A VAL* 3.4 30.7 - - + +
338A ASP* 3.2 15.5 - - + +
339A PHE* 4.0 10.8 - - + -
357A ASP* 1.3 72.2 - - - +
359A LYS* 1.3 69.5 + - - +
360A GLY 3.2 0.2 + - - -
361A THR* 3.2 34.5 + - - +
363A GLU* 3.0 27.0 + - + +
365A TYR* 3.3 23.8 + - + -
404A HIS* 3.3 26.3 - - - -
665A HIS* 4.3 2.4 - - - -
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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