Contacts of the strand formed by residues 397 - 402 (chain I) in PDB entry 4CDC
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 ASP 397 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D TYR* 5.7 0.7 + - - -
333H GLU* 4.5 2.4 - - - +
389I GLY 3.5 4.0 - - - -
390I THR* 2.9 26.0 + - - +
395I GLY 3.3 4.3 + - - +
396I MET* 1.3 92.9 - - + +
398I TYR* 1.3 61.2 + - - +
418I ARG* 3.7 1.2 - - - -
419I ARG* 3.0 59.1 + - + +
420I GLY* 6.1 0.3 - - - -
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Residues in contact with TYR 398 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363H ILE* 3.8 28.3 - - + -
388I TYR* 3.3 1.2 - - - -
389I GLY* 2.7 67.1 + - - -
390I THR 3.5 15.5 + - - -
391I ASP* 3.7 4.7 - - - -
396I MET 3.7 11.0 - - - -
397I ASP* 1.3 75.9 - - - +
399I TRP* 1.3 70.2 + - - +
400I ILE* 3.6 19.9 - - + +
416I ARG* 3.5 40.4 + - + -
417I ILE 3.2 14.6 - - - +
419I ARG* 3.1 16.5 + - - +
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Residues in contact with TRP 399 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333H GLU* 3.7 32.5 - - + -
336H MET* 3.8 24.2 - - + -
337H LYS* 3.8 18.8 - - + -
340H LEU* 4.6 2.5 - - + -
385I LEU* 3.5 38.4 - - + -
387I GLY 3.5 9.6 - - - -
388I TYR* 3.8 9.2 - + + -
398I TYR* 1.3 73.5 - - - +
400I ILE* 1.3 61.8 + - - +
401I VAL* 4.0 2.9 + - + -
415I PHE 3.8 0.2 - - - +
416I ARG* 3.1 27.2 - - - +
417I ILE* 2.8 21.8 + - + +
418I ARG 3.7 17.3 - - - -
419I ARG* 3.4 33.0 - - + +
426I ILE* 4.1 16.5 - - + +
427I GLU* 2.9 28.2 + - + +
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Residues in contact with ILE 400 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211H TRP 3.9 9.4 - - - +
212H ASP* 4.0 17.3 - - + +
214H ARG* 3.4 26.2 - - - +
385I LEU* 3.6 3.1 - - - +
386I VAL* 3.0 37.0 + - + +
387I GLY* 2.8 20.4 + - - +
388I TYR 3.8 19.5 - - - +
398I TYR* 3.6 30.5 - - + +
399I TRP* 1.3 72.0 - - - +
401I VAL* 1.3 62.6 + - - +
414I TYR* 4.3 7.2 - - + -
415I PHE 3.7 5.6 - - - +
416I ARG* 4.3 8.7 - - + -
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Residues in contact with VAL 401 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348H VAL* 4.8 1.6 - - + -
383I VAL* 3.4 35.2 - - + -
384I LEU 3.5 13.2 - - - +
385I LEU* 4.2 8.1 - - + +
399I TRP* 4.0 10.8 - - + +
400I ILE* 1.3 80.1 - - - +
402I LYS* 1.3 61.4 + - - +
414I TYR* 3.2 7.7 - - - +
415I PHE* 2.8 58.2 + - + +
417I ILE* 3.9 28.5 - - + -
426I ILE* 4.2 6.1 - - + -
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Residues in contact with LYS 402 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222H VAL* 3.8 12.4 - - + +
223H SER* 2.8 43.6 + - - -
224H PRO 3.4 14.2 + - - -
225H VAL* 3.8 17.0 - - + +
226H ARG 5.0 0.7 - - - +
241H GLY* 4.7 7.5 - - - -
244H GLU* 4.9 0.4 + - - -
383I VAL* 3.6 5.2 - - - +
384I LEU* 2.8 59.4 + - + +
386I VAL* 4.2 4.2 - - + +
400I ILE 4.4 0.2 + - - -
401I VAL* 1.3 72.7 - - - +
403I ASN* 1.3 70.3 + - - +
414I TYR* 3.4 28.6 - - + +
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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
------------------------------------------------------------
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