Contacts of the strand formed by residues 398 - 404 (chain A) in PDB entry 4PBZ
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 398 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A THR* 3.7 33.0 - - + -
38A HIS 3.7 1.3 - - - -
39A ALA* 4.3 20.9 - - + -
40A LEU* 5.2 0.6 - - - +
372A GLY 5.5 0.7 - - - +
373A HIS* 4.2 9.6 - - - +
374A THR* 5.6 0.9 - - - +
393A VAL* 3.5 3.6 - - - +
394A SER* 3.0 30.6 + - - +
396A ASP* 3.2 32.5 + - - +
397A ASN* 1.3 79.3 - - - +
399A MET* 1.3 62.5 + - - +
400A GLN* 3.8 20.9 - - + +
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Residues in contact with MET 399 (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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36A MET 3.8 0.9 - - - +
37A THR* 3.7 1.6 - - - -
38A HIS* 2.9 51.8 + - + +
40A LEU* 4.1 14.6 - - + -
66A LEU* 4.0 26.7 - - + -
68A LEU* 4.3 20.6 - - + -
82A ALA* 5.8 0.2 - - + -
115A ILE* 3.7 45.7 - - + +
391A CYS* 3.7 19.1 - - - -
392A SER 3.5 4.3 - - - -
393A VAL* 3.9 10.8 - - + -
398A ILE* 1.3 74.9 - - - +
400A GLN* 1.3 66.2 + - - +
401A VAL* 4.6 3.3 - - + +
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Residues in contact with GLN 400 (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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21A TYR* 4.9 2.6 + - - -
24A TRP* 3.8 10.4 - - - -
35A VAL* 5.1 3.4 - - + -
36A MET 3.2 4.0 - - - +
37A THR* 3.6 29.0 + - - +
370A HIS* 2.6 38.4 + - - -
372A GLY* 2.8 32.0 + - - -
373A HIS* 3.7 13.8 + - + +
390A ILE 3.6 0.7 - - - +
391A CYS* 3.2 5.0 - - - -
392A SER 2.8 34.1 + - - +
398A ILE* 3.8 12.9 - - + +
399A MET* 1.3 77.2 - - - +
401A VAL* 1.3 65.5 + - - +
402A TRP* 3.9 12.0 - - + -
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Residues in contact with VAL 401 (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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34A LEU* 4.3 4.8 - - + +
35A VAL* 3.6 1.0 + - - -
36A MET* 2.8 46.3 + - + +
49A TRP* 4.0 15.0 - - + -
84A VAL* 4.6 12.1 - - + -
86A LEU* 4.0 21.5 - - + -
115A ILE* 4.7 11.7 - - + -
389A VAL* 3.9 22.7 - - + -
390A ILE 3.2 4.9 - - - +
391A CYS* 4.3 17.5 - - + -
399A MET* 4.6 7.4 - - + -
400A GLN* 1.3 77.9 - - - +
402A TRP* 1.3 61.5 + - - +
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Residues in contact with TRP 402 (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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32A TYR* 3.6 22.9 - + + -
34A LEU* 3.2 15.5 - - - +
35A VAL* 4.2 9.4 - - + -
342A LEU* 3.9 21.3 - - + -
344A VAL* 4.4 3.4 - - + -
368A PHE* 3.6 26.7 - + - -
370A HIS* 3.5 46.4 + + + -
388A TRP 3.5 2.7 - - - +
389A VAL* 3.3 3.0 - - - -
390A ILE* 2.8 75.7 + - + +
392A SER* 3.1 23.0 + - - -
400A GLN* 3.9 8.7 - - + -
401A VAL* 1.3 80.1 - - - +
403A GLN* 1.3 64.7 + - - +
404A MET* 4.1 13.9 - - + -
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Residues in contact with GLN 403 (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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32A TYR* 3.3 6.5 - - - -
33A ASP* 2.8 47.1 + - - +
34A LEU* 2.9 24.7 + - + +
386A GLU* 5.3 3.0 + - - +
387A PRO 3.0 24.4 + - - -
388A TRP* 3.6 22.6 - - + +
389A VAL* 3.9 16.5 - - + +
402A TRP* 1.3 77.9 - - - +
404A MET* 1.3 66.7 + - - +
409A TYR* 4.6 7.3 + - - +
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Residues in contact with MET 404 (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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31A LEU 3.4 11.4 - - - +
32A TYR* 4.1 3.6 - - - +
33A ASP* 3.8 5.2 - - - +
344A VAL* 4.0 17.5 - - + -
367A LEU* 4.3 4.7 - - + -
368A PHE* 3.4 45.1 - - + -
382A TRP* 6.0 0.2 - - + -
388A TRP* 3.9 28.8 + - + +
402A TRP* 4.1 10.7 - - + -
403A GLN* 1.3 80.9 - - - +
405A ALA* 1.3 63.5 + - - +
406A GLU 3.4 2.1 + - - -
408A ILE* 3.5 30.1 - - + -
409A TYR* 3.6 32.2 + - + -
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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