Contacts of the strand formed by residues 407 - 411 (chain B) in PDB entry 2B7O
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 GLY 407 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B PHE* 3.5 13.7 - - - -
81B LEU* 3.0 17.5 - - - -
363B TRP 3.2 3.2 + - - -
364B GLN* 3.3 8.5 - - - -
365B CYS* 2.9 22.0 + - - +
394B PHE* 3.9 5.9 - - - -
405B PRO 3.5 2.8 - - - -
406B GLY* 1.3 79.8 - - - +
408B ILE* 1.3 65.7 + - - +
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Residues in contact with ILE 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PHE* 4.3 16.4 - - + -
81B LEU 2.9 6.7 + - - +
82B LEU* 3.8 28.0 - - + -
83B GLN 3.0 19.6 + - - -
109B MSE 4.3 9.9 - - + -
113B LEU* 4.4 10.3 - - + -
364B GLN* 2.9 15.9 + - - -
365B CYS* 3.3 12.3 - - + +
367B PRO* 5.3 0.2 - - + -
391B VAL* 4.0 33.9 - - + -
395B PHE* 5.3 1.8 - - + -
407B GLY* 1.3 76.8 - - - +
409B HIS* 1.3 60.9 + - - +
410B VAL* 4.2 20.2 - - + -
452B LEU* 4.7 3.6 - - + -
453B ALA* 5.7 0.9 - - - -
456B VAL* 4.7 16.6 - - + -
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Residues in contact with HIS 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLN* 3.3 35.6 + - + -
126B ARG* 3.0 50.5 + - + -
280B TRP* 3.9 16.7 - + + -
306B LYS* 4.2 16.0 - - - -
335B VAL* 4.4 6.3 - - + -
364B GLN* 3.4 18.6 - - + +
365B CYS 2.8 12.5 + - - +
366B ASP* 3.6 20.8 + - + +
367B PRO* 3.4 20.6 - - - +
368B MSE 4.0 1.1 - - - +
369B HIS* 5.9 0.4 - - - -
408B ILE* 1.3 75.5 - - - +
410B VAL* 1.3 65.9 + - - +
411B GLU* 5.7 0.2 + - - -
703B PEP 4.7 1.1 - - - -
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Residues in contact with VAL 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 5.4 0.4 - - + -
83B GLN 2.8 13.1 + - - +
84B GLY* 3.2 23.5 - - - -
85B GLY 3.5 2.1 + - - -
109B MSE 4.1 15.7 - - + -
126B ARG* 3.6 9.2 - - - -
367B PRO* 4.4 13.0 - - + -
368B MSE 4.2 7.9 - - - -
408B ILE* 4.2 16.6 - - + -
409B HIS* 1.3 81.9 + - - +
411B GLU* 1.3 60.9 + - - +
412B ILE* 2.9 40.8 - - + -
444B LEU* 4.4 2.2 - - + -
452B LEU* 3.6 28.0 - - + -
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Residues in contact with GLU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLY 3.4 3.1 - - - +
87B CYS* 3.7 17.7 - - + +
126B ARG* 3.7 11.4 + - - +
368B MSE 3.4 24.9 - - + +
369B HIS* 2.2 40.4 + - - -
382B ARG* 2.9 23.7 + - - +
409B HIS* 5.7 0.4 + - - +
410B VAL* 1.3 76.3 - - - +
412B ILE* 1.3 62.3 + - - +
441B ASP* 3.7 3.5 - - - +
443B ARG* 3.3 13.5 - - + -
444B LEU* 3.0 20.6 + - - +
701B MN 2.6 23.6 + - - -
703B PEP 3.6 3.5 + - - -
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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