Contacts of the strand formed by residues 369 - 374 (chain B) in PDB entry 4L28
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 ARG 369 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B CYS* 4.6 0.2 - - - -
104B GLU* 2.7 45.6 + - - +
106B LEU* 3.6 20.2 - - + +
244B CYS* 2.9 41.1 + - - +
245B ASP* 5.5 1.6 + - - -
247B LYS* 3.0 34.0 + - + +
248B LEU* 3.9 13.3 - - + +
249B ASP* 3.1 30.9 + - - +
250B MET 3.3 7.3 + - - +
364B LEU* 4.3 3.8 - - - +
367B GLY 5.5 0.7 - - - +
368B GLN* 1.3 78.7 - - - +
370B CYS* 1.3 60.9 + - - +
371B VAL* 4.8 0.2 - - - -
76D ILE* 3.8 19.6 - - - +
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Residues in contact with CYS 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B CYS* 4.3 2.4 - - - -
104B GLU 2.8 10.3 + - - +
105B LEU* 3.5 25.3 - - + +
106B LEU* 2.8 32.3 + - - +
250B MET* 3.3 20.4 - - + -
252B VAL* 3.6 30.3 - - - -
357B ALA* 4.7 1.3 - - - -
361B ALA* 4.2 10.8 - - + -
364B LEU* 3.9 17.9 - - + +
369B ARG* 1.3 73.4 - - - +
371B VAL* 1.3 60.2 + - - +
372B VAL* 4.4 1.6 - - - -
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Residues in contact with VAL 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B MET* 4.4 17.9 - - + -
106B LEU* 3.3 21.1 - - + +
108B LYS* 4.7 6.3 - - + -
240B ILE* 4.5 5.4 - - + -
244B CYS* 4.0 20.4 - - - -
248B LEU* 3.5 27.6 - - + -
250B MET 2.9 9.1 + - - +
251B LEU* 3.4 22.8 - - + +
252B VAL 2.9 26.2 + - - +
369B ARG* 4.8 0.4 - - - -
370B CYS* 1.3 75.2 - - - +
372B VAL* 1.3 70.5 + - - +
373B ILE* 4.7 1.3 - - + -
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Residues in contact with VAL 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ILE* 6.3 0.4 - - + -
105B LEU* 4.1 16.4 - - + -
106B LEU 2.6 14.2 + - - +
107B ALA* 3.3 5.3 - - + -
108B LYS* 2.8 25.8 + - - +
252B VAL* 3.6 12.3 - - + -
353B THR* 3.6 13.0 - - + -
354B VAL* 3.7 13.9 - - + -
357B ALA* 3.6 30.7 - - + -
370B CYS* 4.4 0.2 - - - -
371B VAL* 1.3 78.7 - - - +
373B ILE* 1.3 76.4 + - - +
374B LEU* 3.7 17.2 + - + -
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Residues in contact with ILE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LYS* 3.8 28.5 - - + +
110B GLU* 4.9 8.5 - - + +
118B VAL* 5.5 4.9 - - + -
236B THR* 5.6 1.3 - - + -
240B ILE* 4.3 7.9 - - + -
251B LEU* 4.4 9.9 - - + -
252B VAL 3.0 17.8 + - - +
253B ALA* 4.1 19.1 - - + -
254B SER 5.4 1.1 - - - +
260B THR* 4.7 13.5 - - + -
264B ILE* 4.2 24.2 - - + -
353B THR* 3.6 12.5 + - - +
371B VAL* 4.7 0.7 - - + -
372B VAL* 1.3 78.8 - - - +
374B LEU* 1.3 72.7 + - - +
375B PRO* 3.4 24.6 - - + +
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ALA* 3.7 29.4 - - + -
108B LYS 3.2 11.3 + - - +
109B CYS* 4.2 9.2 - - - -
110B GLU* 3.1 22.4 + - - -
111B PHE* 3.8 20.8 - - + -
338B LEU* 5.0 3.6 - - + -
344B LEU* 3.9 20.9 - - + -
346B CYS* 4.6 9.4 - - - -
350B ALA* 3.6 22.4 - - + -
354B VAL* 4.0 13.5 - - + -
372B VAL* 3.7 16.4 - - + -
373B ILE* 1.3 86.0 - - - +
375B PRO* 1.3 65.8 - - - +
376B ASP 3.3 3.6 + - - -
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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
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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