Contacts of the strand formed by residues 408 - 414 (chain I) in PDB entry 2B4X
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 PHE 408 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239I PHE* 4.5 2.0 - + - -
283I LEU* 3.9 27.8 - - + -
284I ILE 3.2 20.0 - - - +
285I LEU* 4.0 11.9 - - + -
292I LEU* 4.1 6.5 - - - -
320I MET* 4.5 3.8 - - + -
321I PRO* 4.0 21.8 - - + -
323I PHE* 4.0 14.6 - + - -
404I ALA* 4.1 15.3 - - + -
406I ARG 3.3 15.0 - - - +
407I PRO* 1.3 74.5 - - - +
409I LEU* 1.3 82.0 + - - +
410I VAL* 3.9 17.7 - - + -
425I ARG* 3.6 4.2 - - - +
426I VAL* 2.9 59.8 + - + -
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Residues in contact with LEU 409 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I TYR* 3.4 31.9 - - + +
282I VAL 4.3 0.9 - - - -
283I LEU* 3.5 2.8 - - - -
284I ILE* 2.9 42.8 + - + +
292I LEU* 3.9 10.3 - - + -
295I VAL* 4.4 13.5 - - + -
296I GLU* 4.0 21.1 - - + +
299I LEU* 4.8 13.0 - - + -
408I PHE* 1.3 89.4 - - - +
410I VAL* 1.3 62.9 + - - +
411I PHE* 3.8 25.1 - - + -
423I MET* 6.5 0.2 - - + -
424I GLY 3.5 9.4 - - - +
425I ARG* 4.1 9.0 - - + -
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Residues in contact with VAL 410 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I PHE* 5.4 3.6 - - + -
281I MET* 3.7 32.8 - - + -
282I VAL 3.5 4.0 - - - -
283I LEU* 4.1 2.0 - - + -
323I PHE* 4.3 3.8 - - + -
325I ILE* 6.0 0.4 - - + -
373I LEU* 4.6 11.0 - - + -
408I PHE* 3.9 9.4 - - + -
409I LEU* 1.3 80.3 - - - +
411I PHE* 1.3 78.6 + - - +
412I ILE* 4.5 6.1 - - + -
423I MET* 3.2 2.9 - - - +
424I GLY* 3.0 42.3 + - - +
426I VAL* 3.7 30.7 - - + +
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Residues in contact with PHE 411 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281I MET* 3.0 10.7 - - - +
282I VAL* 2.9 54.1 + - + +
284I ILE* 3.8 23.3 - - + -
299I LEU* 5.0 6.3 - - + -
304I LEU* 3.9 32.1 - - + -
409I LEU* 3.8 24.7 - - + -
410I VAL* 1.3 94.7 - - - +
412I ILE* 1.3 66.3 + - - +
413I ARG* 3.8 7.4 - - + +
420I ILE* 4.0 26.2 - - + -
422I PHE 3.5 6.1 - - - +
423I MET* 3.8 29.8 - - + +
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Residues in contact with ILE 412 (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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77I PHE* 4.8 1.3 - - + -
221I PHE* 4.1 20.6 - - + -
274I PHE* 4.3 7.6 - - + -
279I ILE* 4.0 20.4 - - + -
280I THR 3.2 9.6 - - - +
281I MET* 3.8 28.9 - - + -
373I LEU* 4.2 23.6 - - + -
410I VAL* 4.5 2.0 - - + -
411I PHE* 1.3 83.3 - - - +
413I ARG* 1.3 58.4 + - - +
421I ILE* 2.9 31.2 + - + +
422I PHE* 3.0 40.6 + - + +
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Residues in contact with ARG 413 (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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259I ARG* 5.0 2.4 - - - +
271I GLU* 3.2 25.9 + - - -
278I ASP 3.6 0.3 - - - +
279I ILE* 3.4 3.7 - - - +
280I THR* 2.9 41.6 + - - +
282I VAL* 4.4 11.4 - - + +
305I GLN* 5.5 0.8 - - - +
308I LEU* 3.4 45.0 - - - +
411I PHE* 3.8 5.6 - - + -
412I ILE* 1.3 75.9 - - - +
414I GLU* 1.3 60.3 + - - +
415I VAL* 3.7 36.3 + - + +
418I ASN* 3.8 22.0 + - - +
419I THR 2.9 21.7 + - - +
420I ILE* 4.0 15.3 - - + -
421I ILE* 4.3 3.4 - - - -
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Residues in contact with GLU 414 (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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129I ARG 5.7 0.2 - - - +
130I LEU* 4.2 9.2 - - + +
278I ASP* 3.2 18.6 - - - +
279I ILE* 3.5 18.2 - - + -
413I ARG* 1.3 72.4 - - - +
415I VAL* 1.3 59.8 + - - +
416I PRO* 3.4 16.9 - - - +
417I LEU* 2.5 61.6 + - + +
418I ASN* 3.0 3.3 + - - -
419I THR* 2.9 35.6 + - - +
421I ILE* 3.8 15.8 - - + +
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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