Contacts of the strand formed by residues 381 - 390 (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 HIS 381 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228H GLN* 3.5 15.8 + - - -
234H CYS* 3.4 33.7 - - + +
349H ALA* 3.1 6.0 - - - +
350H PHE* 2.9 43.7 + + + +
352H VAL* 3.4 29.6 - - + -
379I THR* 4.8 0.6 - - - -
380I ASN* 1.3 83.6 + - - +
382I ALA* 1.3 62.5 + - - +
383I VAL* 3.5 20.2 - - + +
403I ASN* 2.8 26.3 + - - -
404I SER* 4.1 0.2 - - - -
405I TRP* 3.7 22.5 + + - -
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Residues in contact with ALA 382 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234H CYS* 3.5 36.4 - - - +
235H TYR* 3.7 20.0 - - + +
238H ALA* 3.9 9.5 - - + +
279H PRO* 4.2 12.1 - - + -
348H VAL 3.5 8.3 - - - +
349H ALA* 4.3 4.0 - - + +
381I HIS* 1.3 76.6 + - - +
383I VAL* 1.3 69.8 + - - +
404I SER* 4.5 3.8 + - - -
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Residues in contact with VAL 383 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238H ALA* 3.9 8.9 - - - +
347H ALA* 3.5 4.9 - - - -
348H VAL* 2.9 43.5 + - + +
350H PHE* 3.7 26.0 - - + -
381I HIS* 3.5 23.6 - - + -
382I ALA* 1.3 80.6 - - - +
384I LEU* 1.3 60.4 + - - +
385I LEU 4.1 0.2 - - - -
401I VAL* 3.4 20.9 - - + -
402I LYS 3.6 12.6 - - - +
403I ASN* 3.6 19.3 - - - +
404I SER* 5.1 0.7 - - - +
415I PHE* 4.3 3.4 - - + -
426I ILE* 4.8 0.7 - - + -
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Residues in contact with LEU 384 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222H VAL* 4.4 6.7 - - + -
237H PHE 5.7 0.2 - - - +
238H ALA* 4.0 11.4 - - - +
241H GLY* 3.6 23.8 - - - +
242H MET* 3.5 29.8 - - + +
245H ALA* 4.9 0.2 - - + -
345H PRO* 3.8 11.9 - - + -
346H MET 3.5 28.5 - - - +
347H ALA* 4.1 0.4 - - - +
383I VAL* 1.3 75.0 - - - +
385I LEU* 1.3 62.0 + - - +
386I VAL* 3.5 18.4 + - + -
401I VAL* 3.5 3.0 - - - -
402I LYS* 2.8 59.4 + - + +
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Residues in contact with LEU 385 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336H MET* 3.7 30.5 - - + -
340H LEU* 3.6 16.8 - - + +
345H PRO* 3.2 26.7 - - - +
346H MET* 2.8 36.6 + - + +
348H VAL* 4.1 12.2 - - + +
383I VAL 4.0 1.6 + - - -
384I LEU* 1.3 70.9 - - - +
386I VAL* 1.3 58.7 + - - +
387I GLY 3.7 3.1 - - - +
399I TRP* 3.5 48.7 - - + -
400I ILE 3.6 16.6 - - - +
401I VAL* 4.2 8.1 - - + +
426I ILE* 5.9 1.1 - - + -
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Residues in contact with VAL 386 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211H TRP* 4.5 0.2 - - - -
212H ASP* 3.9 9.8 - - - +
213H TRP* 3.0 32.0 + - + -
214H ARG* 4.4 2.5 - - - +
222H VAL* 4.1 27.8 - - + -
340H LEU* 4.0 8.7 - - - -
345H PRO* 4.3 5.4 - - + -
384I LEU* 3.5 30.3 + - + +
385I LEU* 1.3 78.0 - - - +
387I GLY* 1.3 60.0 + - - +
400I ILE* 3.0 27.4 + - + +
401I VAL 4.7 0.2 - - - +
402I LYS* 4.2 6.7 - - + +
414I TYR* 3.8 22.4 - - + -
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Residues in contact with GLY 387 (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 3.0 13.9 - - - -
212H ASP* 4.2 0.7 - - - -
340H LEU* 3.7 14.9 - - - +
385I LEU* 3.7 7.4 - - - +
386I VAL* 1.3 80.0 - - - +
388I TYR* 1.3 61.2 + - - +
399I TRP* 3.5 4.0 - - - -
400I ILE* 2.8 41.0 + - - +
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Residues in contact with TYR 388 (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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207H LEU* 3.8 9.4 - - - +
208H PRO* 2.5 45.6 + - - +
209H THR 3.4 19.5 - - - -
210H SER* 3.4 4.0 - - - -
211H TRP* 2.7 53.1 + - + +
337H LYS* 3.8 34.5 - - + -
340H LEU* 4.0 15.5 - - + -
341H VAL* 3.7 14.8 - - + +
387I GLY* 1.3 74.5 - - - +
389I GLY* 1.3 60.2 + - - +
398I TYR 3.3 13.9 - - - +
399I TRP* 3.8 8.1 - + + -
400I ILE* 3.8 11.2 - - - +
419I ARG* 3.6 22.0 - - - +
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Residues in contact with GLY 389 (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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209H THR 4.3 3.4 - - - -
210H SER* 4.1 13.5 - - - -
388I TYR* 1.3 78.0 - - - +
390I THR* 1.3 59.8 + - - -
397I ASP* 3.5 0.2 - - - -
398I TYR* 2.7 53.5 + - - -
419I ARG* 3.1 9.0 + - - -
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Residues in contact with THR 390 (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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209H THR* 4.5 15.9 + - - +
210H SER* 5.4 0.6 - - - -
389I GLY* 1.3 74.0 - - - -
391I ASP* 1.3 67.6 + - - +
392I SER* 3.4 4.7 + - - -
395I GLY* 3.4 30.3 - - - +
396I MET 3.4 4.0 - - - +
397I ASP* 2.9 27.6 + - - +
398I TYR* 3.5 9.3 + - - -
419I ARG* 3.9 4.0 + - - -
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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