Contacts of the strand formed by residues 448 - 453 (chain B) in PDB entry 4OMD
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 448 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A ARG* 4.3 1.1 - - - +
446B PRO* 3.9 9.3 + - + +
447B GLN* 1.3 81.6 - - - +
449B LYS* 1.3 62.1 + - - +
477B GLU 4.4 0.8 + - - -
478B PRO* 3.3 26.3 + - - +
479B ASN* 3.9 13.2 - - - +
480B HIS* 2.7 47.6 + - - +
481B ILE* 4.1 8.1 - - + -
570B LEU 3.8 0.2 - - - +
571B TYR* 3.3 5.0 - - - -
572B GLY 2.8 42.7 + - - +
573B THR* 4.4 5.1 - - - +
574B ALA* 3.5 24.1 - - - +
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Residues in contact with LYS 449 (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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269A LEU* 4.4 6.8 + - - +
272A GLU* 2.6 37.7 + - - +
273A ALA* 5.9 0.2 - - - +
276A ARG* 3.8 27.7 - - - +
448B ARG* 1.3 75.9 - - - +
450B CYS* 1.3 61.6 + - - +
451B ILE* 4.2 23.8 + - + +
479B ASN* 3.1 25.1 - - - +
569B VAL* 3.8 19.5 - - + -
570B LEU 3.3 3.6 - - - +
571B TYR* 3.4 28.0 + - + +
602B FMT 2.8 26.0 + - - +
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Residues in contact with CYS 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B LYS* 1.3 74.3 - - - +
451B ILE* 1.3 61.2 + - - +
452B ILE* 4.0 17.0 - - - +
473B ALA* 3.6 8.5 - - - -
474B CYS* 2.0 59.2 - - + -
479B ASN 3.8 9.6 - - - +
481B ILE* 4.1 9.6 - - + +
568B LEU 3.7 1.4 - - - +
569B VAL* 3.6 2.0 - - - -
570B LEU* 2.7 46.3 + - + +
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Residues in contact with ILE 451 (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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234A ALA* 4.0 13.5 - - + -
237A ALA* 3.8 31.2 - - + -
238A ARG* 3.8 36.6 + - + +
269A LEU* 3.9 23.3 - - + -
449B LYS* 4.2 26.0 + - + +
450B CYS* 1.3 76.0 - - - +
452B ILE* 1.3 70.1 + - - +
453B ASP 4.2 0.4 + - - -
474B CYS* 4.5 2.1 - - - -
479B ASN* 5.2 0.6 + - - -
567B THR* 3.6 24.5 - - + -
568B LEU 3.7 2.9 - - - +
569B VAL* 4.5 6.3 - - + +
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Residues in contact with ILE 452 (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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450B CYS* 4.0 15.0 - - - -
451B ILE* 1.3 81.4 - - - +
453B ASP* 1.3 66.4 + - - +
454B ILE* 3.4 22.1 + - + +
469B LYS* 4.6 7.9 - - - -
471B VAL* 3.8 34.5 - - + -
473B ALA* 4.6 3.8 - - - +
474B CYS* 5.3 0.4 - - - +
567B THR* 4.1 2.0 - - - -
568B LEU* 2.8 47.2 + - + +
570B LEU* 3.8 28.7 - - + -
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Residues in contact with ASP 453 (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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232A THR* 3.8 24.8 + - - +
234A ALA* 3.8 16.4 - - + +
238A ARG* 6.3 0.4 - - - +
451B ILE* 4.2 2.2 + - - +
452B ILE* 1.3 75.9 - - - +
454B ILE* 1.3 64.3 + - - +
455B LEU* 3.9 8.9 + - - +
469B LYS* 5.2 4.0 + - - -
565B LYS* 4.1 13.7 - - - +
566B PHE 3.7 6.2 + - - +
567B THR* 2.7 29.8 + - - +
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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